Structures

This page provides a summary of the methods used for structure determination and phasing in riboswitch research. Additionally, we provide a comprehensive list of all the riboswitches included in this collection, along with their respective Protein Data Bank (PDB) entries.

structures

Statistical information

Statistics of structure determination and phasing methods for riboswitches. Left: structure determination for riboswitches (Cryogenic electron microscopy, Cryo-EM; Nuclear magnetic resonance spectroscopy, NMR). Right: The inner circle show cases of molecular replacement (MR) and de novo phasing based on heavy atom derivatives. The outer circle further indicates the heavy atom used for de novo phasing, and the searching model for MR.

drawing


Detail information

This section displays all the PDB entries for the collected riboswitches. Additionally, we provide information on the phase determination for each PDB entry.

Structures



Cofactors

Name PDB Length Description(PDB) Species Phase Determination Structure Determination Res(Å) Year Journal
Adocbl 4GXY 172 RNA structure None SAD-Ir X-RAY DIFFRACTION 3.05 Å 2012 Nat Struct Mol Biol
AqCbl aptamer domain 4FRG 84 Crystal structure of the cobalamin riboswitch aptamer domain Marine metagenome SAD-Ir X-RAY DIFFRACTION 2.95 Å 2012 Nature
AqCbl regulatory element 4FRN 102 Crystal structure of the cobalamin riboswitch regulatory element Marine metagenome MR X-RAY DIFFRACTION 3.43 Å 2012 Nature
cobalamine 6VMY 148 Structure of the B. subtilis cobalamin riboswitch Bacillus subtilis MR (4GXY), MIR-Co, Ir, Ba X-RAY DIFFRACTION 3.25 Å 2020 Nucleic Acids Res
Adocbl 4GMA 210 Crystal structure of the adenosylcobalamin riboswitch Marine metagenome MR X-RAY DIFFRACTION 3.94 Å 2012 Nature
FMN 3F2Q 112 Crystal structure of the FMN riboswitch bound to FMN None MR X-RAY DIFFRACTION 2.95 Å 2009 Nature
FMN 3F2T 112 Crystal structure of the FMN riboswitch bound to FMN, iridium hexamine soak. None MAD-Ir X-RAY DIFFRACTION 3.00 Å 2009 Nature
FMN 3F2W 112 Crystal structure of the FMn riboswitch bound to FMN, Ba2+ soak. None MR X-RAY DIFFRACTION 3.45 Å 2009 Nature
FMN 3F2X 112 Crystal structure of the FMN riboswitch bound to FMN, Cs+ soak. None MR X-RAY DIFFRACTION 3.11 Å 2009 Nature
FMN 3F2Y 112 Crystal structure of the FMN riboswitch bound to FMN, Mn2+ soak. None MR X-RAY DIFFRACTION 3.20 Å 2009 Nature
FMN 3F30 112 Crystal structure of the FMN riboswitch bound to FMN, cobalt hexammine soak. None MR X-RAY DIFFRACTION 3.15 Å 2009 Nature
FMN 3F4E 54 Crystal structure of the FMN riboswitch bound to FMN, split RNA. None MR X-RAY DIFFRACTION 3.05 Å 2009 Nature
FMN 3F4G 54 Crystal structure of the FMN riboswitch bound to riboflavin. None MR X-RAY DIFFRACTION 3.01 Å 2009 Nature
FMN 3F4H 54 Crystal structure of the FMN riboswitch bound to roseoflavin None MR X-RAY DIFFRACTION 3.00 Å 2009 Nature
FMN 2YIF 54 Crystal structure of a F. nucleatum FMN riboswitch - Free state Fusobacterium nucleatum subsp. nucleatum ATCC 25586 MR X-RAY DIFFRACTION 3.30 Å 2011 Nucleic Acids Res
FMN 2YIE 54 Crystal structure of a F. nucleatum FMN riboswitch bound to FMN Fusobacterium nucleatum subsp. nucleatum ATCC 25586 MR X-RAY DIFFRACTION 2.94 Å 2011 Nucleic Acids Res
FMN 5C45 54 Selective Small Molecule Inhibition of the FMN Riboswitch Fusobacterium nucleatum MR X-RAY DIFFRACTION 2.93 Å 2015 Nature
FMN 5KX9 54 Selective Small Molecule Inhibition of the FMN Riboswitch Fusobacterium nucleatum MR X-RAY DIFFRACTION 2.90 Å 2016 RNA Biol
FMN 6BFB 54 Crystal structure of a F. nucleatum FMN riboswitch bound to WG-3 Fusobacterium nucleatum MR X-RAY DIFFRACTION 2.82 Å 2018 ACS Chem Biol
FMN 6DN1 54 CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1151 SPLIT RNA Fusobacterium nucleatum MR X-RAY DIFFRACTION 3.03 Å 2018 ACS Chem Biol
FMN 6DN2 54 CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1354 SPLIT RNA Fusobacterium nucleatum MR X-RAY DIFFRACTION 2.88 Å 2018 ACS Chem Biol
FMN 6DN3 54 CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1555 SPLIT RNA Fusobacterium nucleatum MR X-RAY DIFFRACTION 2.80 Å 2018 ACS Chem Biol
FMN 6WJR 112 Apo structure of the FMN riboswitch aptamer domain in the presence of sulfate Fusobacterium nucleatum MR X-RAY DIFFRACTION 2.70 Å 2020 J Struct Biol X
FMN 6WJS 112 Apo structure of the FMN riboswitch aptamer domain in the presence of phosphate Fusobacterium nucleatum MR X-RAY DIFFRACTION 3.80 Å 2020 J Struct Biol X
THF 3SUY 101 Crystal structure of THF riboswitch, unbound status (Eubacterium) siraeum V10Sc8a MR X-RAY DIFFRACTION 3.21 Å 2011 Proc Natl Acad Sci U S A
THF 3SUX 101 Crystal structure of THF riboswitch, bound with THF (Eubacterium) siraeum V10Sc8a MAD-Ir X-RAY DIFFRACTION 2.90 Å 2011 Proc Natl Acad Sci U S A
THF 3SUH 101 Crystal structure of THF riboswitch, bound with 5-formyl-THF (Eubacterium) siraeum V10Sc8a MR X-RAY DIFFRACTION 2.65 Å 2011 Proc Natl Acad Sci U S A
THF 3SD3 89 The structure of the tetrahydrofolate riboswitch containing a U25C mutation None SAD-Ir X-RAY DIFFRACTION 1.95 Å 2011 Structure
THF 4LVV 89 Structure of the THF riboswitch None SAD-Ir X-RAY DIFFRACTION 2.10 Å 2014 Chem Biol
THF 4LVZ 89 Structure of the THF riboswitch bound to 2,6-diaminopurine None MR X-RAY DIFFRACTION 1.77 Å 2014 Chem Biol
THF 4LVW 89 Structure of the THF riboswitch bound to 7-deazaguanine None MR X-RAY DIFFRACTION 1.77 Å 2014 Chem Biol
THF 4LVX 89 Structure of the THF riboswitch bound to tetrahydrobiopterin None MR X-RAY DIFFRACTION 1.90 Å 2014 Chem Biol
THF 4LVY 89 Structure of the THF riboswitch bound to pemetrexed None MR X-RAY DIFFRACTION 2.00 Å 2014 Chem Biol
THF 4LW0 89 Structure of the THF riboswitch bound to adenine None MR X-RAY DIFFRACTION 1.89 Å 2014 Chem Biol
THF 7KD1 89 Apo structure of the THF riboswitch aptamer domain Streptococcus mutans UA159 MR X-RAY DIFFRACTION 1.90 Å 2021 J Struct Biol
THF 6Q57 89 X-ray crystal structure of the tetrahydrofolate riboswitch aptamer bound to 5-deazatetrahydropterin Streptococcus mutans UA159 MR X-RAY DIFFRACTION 2.72 Å None To be published
THF-II 7WI9 50 The THF-II riboswitch bound to THF and soaking with SeUrea Mesorhizobium loti SAD-Se X-RAY DIFFRACTION 2.98 Å 2023 Nucleic Acids Res
THF-II 7WIA 50 The apo-form of THF-II C22G riboswitch Mesorhizobium loti MR X-RAY DIFFRACTION 3.22 Å 2023 Nucleic Acids Res
THF-II 7WIB 50 The THF-II riboswitch bound to THF Mesorhizobium loti MR X-RAY DIFFRACTION 2.83 Å 2023 Nucleic Acids Res
THF-II 7WIE 50 The THF-II riboswitch bound to 7DG Mesorhizobium loti MR X-RAY DIFFRACTION 2.90 Å 2023 Nucleic Acids Res
THF-II 7WIF 50 The THF-II riboswitch bound to H4B Mesorhizobium loti MR X-RAY DIFFRACTION 2.86 Å 2023 Nucleic Acids Res
THF-II 7WII 50 The THF-II riboswitch bound to NPR Mesorhizobium loti MR X-RAY DIFFRACTION 2.75 Å 2023 Nucleic Acids Res
TPP 2GDI 80 Crystal structure of thiamine pyrophosphate-specific riboswitch in complex with thiamine pyrophosphate None MAD-Os X-RAY DIFFRACTION 2.05 Å 2006 Nature
TPP 2CKY 77 Structure of the Arabidopsis thaliana thiamine pyrophosphate riboswitch with its regulatory ligand Arabidopsis thaliana MAD-Os X-RAY DIFFRACTION 2.90 Å 2006 Science
TPP 2HOJ 83 Crystal structure of an E. coli thi-box riboswitch bound to thiamine pyrophosphate, manganese ions None MR (2CKY) X-RAY DIFFRACTION 2.50 Å 2006 Structure
TPP 2HOK 83 Crystal structure of an E. coli thi-box riboswitch bound to thiamine pyrophosphate, calcium ions None MR X-RAY DIFFRACTION 3.20 Å 2006 Structure
TPP 2HOL 83 Crystal structure of an E. coli thi-box riboswitch bound to thiamine pyrophosphate, barium ions None MR X-RAY DIFFRACTION 2.90 Å 2006 Structure
TPP 2HOM 83 Crystal structure of an E. coli thi-box riboswitch bound to thiamine monophosphate None MR X-RAY DIFFRACTION 2.89 Å 2006 Structure
TPP 2HOO 83 Crystal structure of an E. coli thi-box riboswitch bound to benfotiamine None MR X-RAY DIFFRACTION 3.00 Å 2006 Structure
TPP 2HOP 83 Crystal structure of an E. coli thi-box riboswitch bound to pyrithiamine None MR X-RAY DIFFRACTION 3.30 Å 2006 Structure
TPP 3D2X 77 Structure of the thiamine pyrophosphate-specific riboswitch bound to oxythiamine pyrophosphate Arabidopsis thaliana MR X-RAY DIFFRACTION 2.50 Å 2008 J Am Chem Soc
TPP 3D2V 77 Structure of the eukaryotic TPP-specific riboswitch bound to the antibacterial compound pyrithiamine pyrophosphate Arabidopsis thaliana MR X-RAY DIFFRACTION 2.00 Å 2008 J Am Chem Soc
TPP 3D2G 77 Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch Arabidopsis thaliana MR X-RAY DIFFRACTION 2.25 Å 2008 J Am Chem Soc
TPP 3K0J 96 Crystal structure of the E. coli ThiM riboswitch in complex with thiamine pyrophosphate and the U1A crystallization module Homo sapiens MR X-RAY DIFFRACTION 3.10 Å 2010 RNA
TPP 4NYA 80 Crystal structure of the E. coli thiM riboswitch in complex with 5-(azidomethyl)-2-methylpyrimidin-4-amine Escherichia coli MR X-RAY DIFFRACTION 2.65 Å 2014 Chem Biol
TPP 4NYD 83 Crystal structure of the E. coli thiM riboswitch in complex with hypoxanthine Escherichia coli MR X-RAY DIFFRACTION 2.90 Å 2014 Chem Biol
TPP 4NYC 83 Crystal structure of the E. coli thiM riboswitch in complex with thieno[2,3-b]pyrazin-7-amine Escherichia coli MR X-RAY DIFFRACTION 3.15 Å 2014 Chem Biol
TPP 4NYB 83 Crystal structure of the E. coli thiM riboswitch in complex with (4-(1,2,3-thiadiazol-4-yl)phenyl)methanamine Escherichia coli MR X-RAY DIFFRACTION 3.10 Å 2014 Chem Biol
TPP 4NYG 83 Crystal structure of the E. coli thiM riboswitch in complex with thiamine Escherichia coli MR X-RAY DIFFRACTION 3.05 Å 2014 Chem Biol
TPP 7TD7 83 Crystal structure of an E. coli thiM riboswitch bound to thiamine, manganese ions Escherichia coli MR X-RAY DIFFRACTION 2.95 Å 2022 ACS Chem Biol
TPP 7TDA 83 Crystal structure of the E. coli thiM riboswitch in complex with thiamine pyrophosphate, manganese ions Escherichia coli MR X-RAY DIFFRACTION 2.25 Å 2022 ACS Chem Biol
TPP 7TDB 83 Crystal structure of the E. coli thiM riboswitch in complex with thiamine bisphosphonate, manganese ions Escherichia coli MR X-RAY DIFFRACTION 2.56 Å 2022 ACS Chem Biol
TPP 7TDC 83 Crystal structure of the E. coli thiM riboswitch in complex with thiamine bisphosphonate, calcium ions Escherichia coli MR X-RAY DIFFRACTION 2.46 Å 2022 ACS Chem Biol
TPP 7TZR 80 Crystal structure of the E. coli thiM riboswitch bound to N-methyl-1-(quinoxalin-6-yl)methanamine (compound 16) Escherichia coli MR X-RAY DIFFRACTION 2.70 Å 2022 Proc Natl Acad Sci U S A
TPP 7TZS 80 Crystal structure of the E. coli thiM riboswitch in complex with quinoxalin-6-ylmethanamine (compound 17) Escherichia coli MR X-RAY DIFFRACTION 2.21 Å 2022 Proc Natl Acad Sci U S A
TPP 7TZT 83 Crystal structure of the E. coli thiM riboswitch in complex with N1,N1-dimethyl-N2-(quinoxalin-6-ylmethyl)ethane-1,2-diamine (linked compound 37) Escherichia coli MR X-RAY DIFFRACTION 2.96 Å 2022 Proc Natl Acad Sci U S A
TPP 7TZU 83 Crystal structure of the E. coli thiM riboswitch bound to 1-(4-(piperazin-1-yl)pyridin-3-yl)-N-(quinoxalin-6-ylmethyl)methanamine (linked compound 38) Escherichia coli MR X-RAY DIFFRACTION 2.87 Å 2022 Proc Natl Acad Sci U S A
TPP 8F4O 83 Apo structure of the TPP riboswitch aptamer domain Escherichia coli MR X-RAY DIFFRACTION 3.10 Å 2023 To be published
SAM-I 2GIS 94 Structure of the S-adenosylmethionine riboswitch mRNA regulatory element None MAD-Ir X-RAY DIFFRACTION 2.90 Å 2006 Nature
SAM-I 3GX2 94 TteSAM-I riboswitch variant A94GU34C bound to sinefungin None MR X-RAY DIFFRACTION 2.90 Å 2010 J Mol Biol
SAM-I 3GX3 94 Crystal structure of the T. tengcongensis SAM-I riboswitch variant U34C/A94G bound with SAH None MR X-RAY DIFFRACTION 2.70 Å 2010 J Mol Biol
SAM-I 3GX5 94 Crystal structure of T. tencongensis SAM-I riboswitch variant A94G/U34 bound with SAM None MR X-RAY DIFFRACTION 2.40 Å 2010 J Mol Biol
SAM-I 3GX6 94 Crystal structure of the T. tengcongensis SAM-I riboswitch variant U34C/A94G bound with SAM in manganese chloride None MR X-RAY DIFFRACTION 2.80 Å 2010 J Mol Biol
SAM-I 3GX7 94 Crystal structure of the T. tengcongensis SAM-I riboswitch variant U34C/A94G mutant A6C/U7G/A87C/U88G bound with SAM None MR X-RAY DIFFRACTION 2.95 Å 2010 J Mol Biol
SAM-I 3IQN 94 Free-state structural transitions of the SAM-I riboswitch None MR X-RAY DIFFRACTION 2.70 Å 2010 Structure
SAM-I 3IQP 94 SAM-I riboswitch from T. tencongensis variant A94G apo form None MR X-RAY DIFFRACTION 2.90 Å 2010 Structure
SAM-I 3IQR 94 SAM-I riboswitch from T. tencongensis variant A94G bound with SAM None MR X-RAY DIFFRACTION 2.55 Å 2010 Structure
SAM-I 4KQY 119 Bacillus subtilis yitJ S box/SAM-I riboswitch Bacillus subtilis subsp. subtilis str. BSP1 MR X-RAY DIFFRACTION 3.02 Å 2010 J Mol Biol
SAM-I 2YGH 95 SAM-I riboswitch with a G2nA mutation in the Kink turn in complex with S-adenosylmethionine Caldanaerobacter subterraneus subsp. tengcongensis MR X-RAY DIFFRACTION 2.60 Å 2011 Structure
SAM-I 2YDH 94 Crystal structure of the SAM-I riboswitch A94G U34 G18U G19U variant in complex with SAM Caldanaerobacter subterraneus subsp. tengcongensis MR X-RAY DIFFRACTION 2.90 Å 2011 Structure
SAM-I 4AOB 94 SAM-I riboswitch containing the T. solenopsae Kt-23 in complex with S- adenosyl methionine Caldanaerobacter subterraneus subsp. tengcongensis MR X-RAY DIFFRACTION 2.95 Å 2012 RNA
SAM-I 4B5R 94 SAM-I riboswitch bearing the H. marismortui K-t-7 Caldanaerobacter subterraneus subsp. tengcongensis MR X-RAY DIFFRACTION 2.95 Å 2013 RNA
SAM-I 7EAF 94 Crystal structure of SAM-I riboswitch with the Actinomyces-1 k-turn Caldanaerobacter subterraneus subsp. tengcongensis MR X-RAY DIFFRACTION 2.85 Å 2021 Nucleic Acids Res
SAM-I 7EAG 19 Crystal structure of the RAGATH-18 k-turn Clostridium perfringens SM101 MR X-RAY DIFFRACTION 2.50 Å 2021 Nucleic Acids Res
SAM-I/IV 4L81 96 Structure of the SAM-I/IV riboswitch (env87(deltaU92, deltaG93)) None MR X-RAY DIFFRACTION 2.95 Å 2014 Proc Natl Acad Sci U S A
SAM-I/IV 4OQU 97 Structure of the SAM-I/IV riboswitch (env87(deltaU92)) None MR X-RAY DIFFRACTION 3.20 Å 2014 Proc Natl Acad Sci U S A
SAM-II 2QWY 52 SAM-II riboswitch bound to S-adenosylmethionine None SAD-Cs / SIRAS-Cs X-RAY DIFFRACTION 2.80 Å 2008 Nat Struct Mol Biol
SAM-III 3E5C 53 Crystal Structure of the SMK box (SAM-III) Riboswitch with SAM None SAD-Ir X-RAY DIFFRACTION 2.25 Å 2008 Nat Struct Mol Biol
SAM-III 3E5E 53 Crystal Structures of the SMK box (SAM-III) Riboswitch with SAH None MR X-RAY DIFFRACTION 2.90 Å 2008 Nat Struct Mol Biol
SAM-III 3E5F 53 Crystal Structures of the SMK box (SAM-III) Riboswitch with Se-SAM None MR X-RAY DIFFRACTION 2.70 Å 2008 Nat Struct Mol Biol
SAM-III 6C27 47 SAM-III riboswitch ON-state Enterococcus faecalis MR X-RAY DIFFRACTION 3.60 Å None To be published
SAM-IV 6UES 119 Apo SAM-IV Riboswitch Mycobacterium sp. MCS None ELECTRON MICROSCOPY 3.70 2019 Nat Commun
SAM-IV 6UET 119 SAM-bound SAM-IV riboswitch Mycobacterium sp. MCS None ELECTRON MICROSCOPY 4.10 2019 Nat Commun
SAM-V 6FZ0 53 Crystal structure of the metY SAM V riboswitch Candidatus Pelagibacter ubique HTCC1062 SAD-Br X-RAY DIFFRACTION 2.50 Å 2018 NAR
SAM-VI 6LAS 55 the wildtype SAM-VI riboswitch bound to SAM Bifidobacterium angulatum', 'Homo sapiens SAD-Se-U1A X-RAY DIFFRACTION 2.71 Å 2019 Nat Commun
SAM-VI 6LAU 55 the wildtype SAM-VI riboswitch bound to SAH Bifidobacterium angulatum', 'Homo sapiens MR X-RAY DIFFRACTION 3.11 Å 2019 Nat Commun
SAM-VI 6LAX 55 the mutant SAM-VI riboswitch (U6C) bound to SAM Bifidobacterium angulatum', 'Homo sapiens MR X-RAY DIFFRACTION 2.70 Å 2019 Nat Commun
SAM-VI 6LAZ 55 the wildtype SAM-VI riboswitch bound to a N-mustard SAM analog M1 Bifidobacterium angulatum', 'Homo sapiens MR X-RAY DIFFRACTION 2.76 Å 2019 Nat Commun
SAM-SAH 6HAG 43 The structure of the SAM/SAH-binding riboswitch. Pseudomonadota None SOLUTION NMR None 2019 Nucleic Acids Res
SAM-SAH 6YL5 35 Crystal structure of the SAM-SAH riboswitch with SAH Roseobacter sp. SAD-Br X-RAY DIFFRACTION 1.70 Å 2020 Nucleic Acids Res
SAM-SAH 6YLB 26 Crystal structure of the SAM-SAH riboswitch with SAM Roseobacter sp. MR X-RAY DIFFRACTION 2.12 Å 2020 Nucleic Acids Res
SAM-SAH 6YMI 26 Crystal structure of the SAM-SAH riboswitch with AMP. Roseobacter sp. MR X-RAY DIFFRACTION 2.50 Å 2020 Nucleic Acids Res
SAM-SAH 6YMJ 26 Crystal structure of the SAM-SAH riboswitch with adenosine. Roseobacter sp. MR X-RAY DIFFRACTION 2.04 Å 2020 Nucleic Acids Res
SAM-SAH 6YMK 26 Crystal structure of the SAM-SAH riboswitch with AMP Roseobacter sp. MR X-RAY DIFFRACTION 2.03 Å 2020 Nucleic Acids Res
SAM-SAH 6YML 26 Crystal structure of the SAM-SAH riboswitch with decarboxylated SAH Roseobacter sp. MR X-RAY DIFFRACTION 2.17 Å 2020 Nucleic Acids Res
SAM-SAH 6YMM 9 Crystal structure of the SAM-SAH riboswitch with SAM from space group P312 Roseobacter sp. MR X-RAY DIFFRACTION 2.20 Å 2020 Nucleic Acids Res
SAH 3NPN 54 Structure of the s-adenosylhomocysteine riboswitch at 3.0A Ralstonia solanacearum SAD-Ir X-RAY DIFFRACTION 2.79 Å 2010 RNA
SAH 3NPQ 54 Structure of the S-adenosylhomocysteine riboswitch at 2.18 A Ralstonia solanacearum MR X-RAY DIFFRACTION 2.18 Å 2010 RNA
NAD+-I 6TB7 52 Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Adenosine monophosphate (AMP) Candidatus Koribacter versatilis Ellin345 MR X-RAY DIFFRACTION 2.53 Å 2020 RNA
NAD+-I (domain I) 6TF0 52 Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Nicotinamide adenine dinucleotide, reduced (NADH) Candidatus Koribacter versatilis Ellin345 SAD-Br X-RAY DIFFRACTION 2.10 Å 2020 RNA
NAD+-I 6TF1 52 Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Adenosine diphosphate (ADP) Candidatus Koribacter versatilis Ellin345 MR X-RAY DIFFRACTION 2.40 Å 2020 RNA
NAD+-I 6TF2 52 Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Adenosine 5-triphosphate (ATP) Candidatus Koribacter versatilis Ellin345 MR X-RAY DIFFRACTION 2.55 Å 2020 RNA
NAD+-I 6TF3 52 Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Cordycepin 5-triphosphate (3-dATP) Candidatus Koribacter versatilis Ellin345 MR X-RAY DIFFRACTION 2.66 Å 2020 RNA
NAD+-I 6TFE 52 Crystal structure of the ADP-binding domain of the NAD+ riboswitch with N6-Methyl-adenosine-5'-triphosphate (m6ATP) Candidatus Koribacter versatilis Ellin345 MR X-RAY DIFFRACTION 2.30 Å 2020 RNA
NAD+-I 6TFF 52 Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Nicotinamide adenine dinucleotide (NAD+) Candidatus Koribacter versatilis Ellin345 MR X-RAY DIFFRACTION 2.52 Å 2020 RNA
NAD+-I 6TFG 52 Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Adenosine 3-phosphate 5-phosphosulfate (APPS) Candidatus Koribacter versatilis Ellin345 MR X-RAY DIFFRACTION 2.45 Å 2020 RNA
NAD+-I 6TFH 52 Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Nicotinamide adenine dinucleotide, reduced (NADH); soaking with Manganese(II) (Mn2+) Candidatus Koribacter versatilis Ellin345 MR X-RAY DIFFRACTION 2.95 Å 2020 RNA
NAD+-I (domain I) 7D7V 92 Crystal Structure of the Domain1 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+) and U1A protein Acidobacterium capsulatum ATCC 51196', 'Homo sapiens SAD-Se-U1A X-RAY DIFFRACTION 2.80 Å 2020 Nucleic Acids Res
NAD+-I 7D7W 51 Crystal Structure of the Domain1 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+) synthetic construct MR X-RAY DIFFRACTION 2.39 Å 2020 Nucleic Acids Res
NAD+-I 7D7X 51 Crystal Structure of the Domain1 of NAD+ Riboswitch with adenosine diphosphate (ADP) synthetic construct MR X-RAY DIFFRACTION 2.63 Å 2020 Nucleic Acids Res
NAD+-I 7D7Y 51 Crystal Structure of the Domain1 of NAD+ Riboswitch with adenosine triphosphate (ATP) synthetic construct MR X-RAY DIFFRACTION 2.80 Å 2020 Nucleic Acids Res
NAD+-I 7D7Z 51 Crystal Structure of the Domain1 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+), soaked in Mn2+ synthetic construct MR X-RAY DIFFRACTION 2.60 Å 2020 Nucleic Acids Res
NAD+-I (domain II) 7D81 50 Crystal Structure of the Domain2 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+) Acidobacteriaceae bacterium KBS 83 MR X-RAY DIFFRACTION 2.10 Å 2020 Nucleic Acids Res
NAD+-I 7D82 50 Crystal Structure of the Domain2 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+), soaked in Mn2+ Acidobacteriaceae bacterium KBS 83 MR X-RAY DIFFRACTION 2.49 Å 2020 Nucleic Acids Res
NAD+-II 8HB1 24 Crystal structure of NAD-II riboswitch (two strands) with NMN Streptococcus parasanguinis SAD-Br X-RAY DIFFRACTION 2.23 Å 2023 Nucleic Acids Res
NAD+-II 8HB3 24 Crystal structure of NAD-II riboswitch (two strands) with NR Streptococcus parasanguinis MR X-RAY DIFFRACTION 2.87 Å 2023 Nucleic Acids Res
NAD+-II 8HB8 55 Crystal structure of NAD-II riboswitch (single strand) with NMN Streptococcus parasanguinis MR X-RAY DIFFRACTION 2.30 Å 2023 Nucleic Acids Res
NAD+-II 8HBA 56 Crystal structure of NAD-II riboswitch (single strand) with NAD Streptococcus parasanguinis MR X-RAY DIFFRACTION 2.64 Å 2023 Nucleic Acids Res
NAD+-II 8I3Z 24 Crystal structure of NAD-II riboswitch (two strands) with NMN at 1.67 angstrom Streptococcus parasanguinis MR X-RAY DIFFRACTION 1.67 Å 2023 Nucleic Acids Res

RNA derivatives

Name PDB Length Description(PDB) Species Phase Determination Structure Determination Res(Å) Year Journal
Xanthine-I 7ELP 45 Crystal structure of xanthine riboswitch with xanthine, iridium hexammine soak Ideonella sp. B508-1 SAD-Ir X-RAY DIFFRACTION 2.79 Å 2021 Nucleic Acids Res
Xanthine-I 7ELQ 45 Crystal structure of xanthine riboswitch with xanthine, manganese saok Ideonella sp. B508-1 MR X-RAY DIFFRACTION 2.60 Å 2021 Nucleic Acids Res
Xanthine-I 7ELR 45 Crystal structure of xanthine riboswitch with xanthine Ideonella sp. B508-1 MR X-RAY DIFFRACTION 2.66 Å 2021 Nucleic Acids Res
Xanthine-I 7ELS 45 Crystal structure of xanthine riboswitch with 8-azaxanthine Ideonella sp. B508-1 MR X-RAY DIFFRACTION 3.00 Å 2021 Nucleic Acids Res
2'-dG-I 3SLM 68 Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'-deoxyguanosine-5'-monophosphate None MR X-RAY DIFFRACTION 2.70 Å 2011 Nat Chem Biol
2'-dG-I 3SKW 66 Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, cesium soak None MR X-RAY DIFFRACTION 2.95 Å 2011 Nat Chem Biol
2'-dG-I 3SKR 66 Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, cobalt Hexammine soak None MR X-RAY DIFFRACTION 3.10 Å 2011 Nat Chem Biol
2'-dG-I 3SKL 66 Crystal structure of the 2'- deoxyguanosine riboswitch bound to 2'-deoxyguanosine, iridium hexammine soak None MR X-RAY DIFFRACTION 2.90 Å 2011 Nat Chem Biol
2'-dG-I 3SKI 68 Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'-deoxyguanosine None SAD-Ir X-RAY DIFFRACTION 2.30 Å 2011 Nat Chem Biol
2'-dG-I 3SKT 66 Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, manganese Soak None MR X-RAY DIFFRACTION 3.10 Å 2011 Nat Chem Biol
2'-dG-I 3SLQ 68 Crystal structure of the 2'- Deoxyguanosine riboswitch bound to guanosine-5'-monophosphate None MR X-RAY DIFFRACTION 2.50 Å 2011 Nat Chem Biol
2'-dG-I 3SKZ 68 Crystal structure of the 2'- deoxyguanosine riboswitch bound to guanosine None MR X-RAY DIFFRACTION 2.60 Å 2011 Nat Chem Biol
2'-dG-II 6P2H 69 Structural basis for 2'-deoxyguanosine recognition by the 2'-dG-II class of riboswitches Synthetic construct MR (4FE5) X-RAY DIFFRACTION 2.80 Å 2019 NAR
PreQ1-I 3K1V 34 Cocrystal structure of a mutant class-I preQ1 riboswitch None MR X-RAY DIFFRACTION 2.20 Å 2009 Nat Struct Mol Biol
PreQ1-I 3FU2 34 Cocrystal structure of a class-I preQ1 riboswitch None MR (Fragments) X-RAY DIFFRACTION 2.85 Å 2009 Nat Struct Mol Biol
PreQ1-I 3GCA 33 The structural basis for recognition of the preQ0 metabolite by an unusually small riboswitch aptamer domain None MAD-Os X-RAY DIFFRACTION 2.75 Å 2009 J Biol Chem
PreQ1-I 2L1V 36 Solution structure of a preQ1 riboswitch (Class I) aptamer bound to preQ1 None None SOLUTION NMR None 2009 Mol Cell
PreQ1-I 3Q50 33 Structural analysis of a class I PreQ1 riboswitch aptamer in the metabolite-bound state None MR X-RAY DIFFRACTION 2.75 Å 2011 J Biol Chem
PreQ1-I 3Q51 33 Structural analysis of a class I PreQ1 riboswitch aptamer in the metabolite-free state. None MR X-RAY DIFFRACTION 2.85 Å 2011 J Biol Chem
PreQ1-I 6E1S 33 Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 1: 2-[(dibenzo[b,d]furan-2-yl)oxy]ethan-1-amine Caldanaerobacter subterraneus subsp. tengcongensis MR X-RAY DIFFRACTION 1.80 Å 2019 Nat Commun
PreQ1-I 6E1T 33 Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 1: 2-[(dibenzo[b,d]furan-2-yl)oxy]ethan-1-amine Caldanaerobacter subterraneus subsp. tengcongensis MR X-RAY DIFFRACTION 1.80 Å 2019 Nat Commun
PreQ1-I 6E1U 33 Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 2: 2-[(dibenzo[b,d]furan-2-yl)oxy]-N,N-dimethylethan-1-amine Caldanaerobacter subterraneus subsp. tengcongensis MR X-RAY DIFFRACTION 1.94 Å 2019 Nat Commun
PreQ1-I 6E1V 33 Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 3: 2-[(9H-carbazol-3-yl)oxy]-N,N-dimethylethan-1-amine Caldanaerobacter subterraneus subsp. tengcongensis MR X-RAY DIFFRACTION 2.56 Å 2019 Nat Commun
PreQ1-I 6E1W 33 Crystal structure of a class I PreQ1 riboswitch complexed with PreQ1 Caldanaerobacter subterraneus subsp. tengcongensis MR X-RAY DIFFRACTION 1.69 Å 2019 Nat Commun
PreQ1-I 6VUH 33 APO PreQ1 riboswitch aptamer grown in Mn2+ Caldanaerobacter subterraneus subsp. tengcongensis MR X-RAY DIFFRACTION 2.00 Å 2020 Nucleic Acids Res
PreQ1-I 6VUI 33 Metabolite-bound PreQ1 riboswitch with Mn2+ Caldanaerobacter subterraneus subsp. tengcongensis MR X-RAY DIFFRACTION 2.68 Å 2020 Nucleic Acids Res
PreQ1-I 7E9E 33 Crystal structure of a class I PreQ1 riboswitch aptamer (ab13-14) complexed with a cognate ligand-derived photoaffinity probe Caldanaerobacter subterraneus subsp. tengcongensis MR X-RAY DIFFRACTION 1.57 Å 2021 Nat Commun
PreQ1-I 7E9I 33 Crystal structure of a class I PreQ1 riboswitch aptamer (wild-type) complexed with a cognate ligand-derived photoaffinity probe Caldanaerobacter subterraneus subsp. tengcongensis MR X-RAY DIFFRACTION 2.80 Å 2021 Nat Commun
PreQ1-I 7REX 34 PreQ1-1 (type-1) riboswitch in complex with tandem stacked metabolites Carnobacterium antarcticum MR X-RAY DIFFRACTION 2.60 Å 2022 Nat Commun
PreQ1-II 4JF2 77 Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold Lacticaseibacillus rhamnosus SAD-Cs X-RAY DIFFRACTION 2.28 Å 2013 Nat Chem Biol
PreQ1-II 2MIY 59 Solution NMR structure of a preQ1 Class II riboswitch from Streptococcus pneumoniae None None SOLUTION NMR None 2014 Proc Natl Acad Sci U S A
PreQ1-II 5D5L 77 PreQ1-II riboswitch with an engineered G-U wobble pair bound to Cs+ Lacticaseibacillus rhamnosus LOCK908 None X-RAY DIFFRACTION 2.50 Å None To be published
preQ1-III 4RZD 101 Crystal Structure of a PreQ1 Riboswitch Faecalibacterium prausnitzii SIRAS-Cs X-RAY DIFFRACTION 2.75 Å 2015 Proc Natl Acad Sci U S A
preQ1-III 6XKO 101 Class III PreQ1 riboswitch mutant A84G Faecalibacterium prausnitzii None X-RAY DIFFRACTION 2.75 Å None To be published
preQ1-III 6XKN 101 Class III PreQ1 riboswitch mutant A52G Faecalibacterium prausnitzii None X-RAY DIFFRACTION 2.73 Å None To be published

RNA precursors

Name PDB Length Description(PDB) Species Phase Determination Structure Determination Res(Å) Year Journal
Adenine 1Y26 71 A-riboswitch-adenine complex Vibrio vulnificus SIRAS-Ba X-RAY DIFFRACTION 2.10 Å 2004 Chem Biol
Adenine 3IVN 70 Structure of the U65C mutant A-riboswitch aptamer from the Bacillus subtilis pbuE operon Bacillus subtilis MR X-RAY DIFFRACTION 2.80 Å 2010 Nucleic Acids Res
Adenine 4TZY 71 Vibrio vulnificus Adenine Riboswitch Variant, grown in both Sr2+ and Mg2+ Vibrio vulnificus MR X-RAY DIFFRACTION 2.57 Å 2014 Structure
Adenine 4TZX 71 Vibrio Vulnificus Adenine Riboswitch variant, grown in Mg2+ Vibrio vulnificus MR X-RAY DIFFRACTION 2.01 Å 2014 Structure
Adenine 4LX5 71 X-ray crystal structure of the M6" riboswitch aptamer bound to pyrimido[4,5-d]pyrimidine-2,4-diamine (PPDA) Vibrio vulnificus MR X-RAY DIFFRACTION 2.13 Å 2014 J Am Chem Soc
Adenine 4LX6 71 X-ray crystal structure of the M6C" riboswitch aptamer bound to 2-aminopyrimido[4,5-d]pyrimidin-4(3H)-one (PPAO) Vibrio vulnificus MR X-RAY DIFFRACTION 2.15 Å 2014 J Am Chem Soc
Adenine 4XNR 71 Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized by Position-selective Labeling of RNA (PLOR), in Complex with Adenine Vibrio vulnificus MR X-RAY DIFFRACTION 2.21 Å 2015 Nature
Adenine 5E54 71 Two apo structures of the adenine riboswitch aptamer domain determined using an X-ray free electron laser Vibrio vulnificus MR X-RAY DIFFRACTION 2.30 Å 2017 Nature
Adenine 5SWE 71 Ligand-bound structure of adenine riboswitch aptamer domain converted in crystal from its ligand-free state using ligand mixing serial femtosecond crystallography Vibrio vulnificus MR X-RAY DIFFRACTION 3.00 Å 2017 Nature
Adenine 5SWD 71 Structure of the adenine riboswitch aptamer domain in an intermediate-bound state Vibrio vulnificus MR X-RAY DIFFRACTION 2.50 Å 2017 Nature
Adenine 5UZA 71 Adenine riboswitch aptamer domain labelled with iodo-uridine by position-selective labelling of RNA (PLOR) Vibrio vulnificus MR X-RAY DIFFRACTION 2.22 Å 2018 Nat Protoc
Adenine 6VWV 71 Transitional unit cell 2 of adenine riboswitch aptamer crystal phase transition upon ligand binding Vibrio vulnificus MR X-RAY DIFFRACTION 3.00 Å 2021 Nat Commun
Adenine 6VWT 71 Transitional unit cell 1 of adenine riboswitch aptamer crystal phase transition upon ligand binding Vibrio vulnificus MR X-RAY DIFFRACTION 3.03 Å 2021 Nat Commun
Guanine 1Y27 68 G-riboswitch-guanine complex Bacillus subtilis MR X-RAY DIFFRACTION 2.40 Å 2004 Chem Biol
Guanine 4FE5 67 Crystal structure of the xpt-pbuX guanine riboswitch aptamer domain in complex with hypoxanthine None SAD-Co X-RAY DIFFRACTION 1.32 Å 2004 Nature
Guanine 2B57 65 Guanine Riboswitch C74U mutant bound to 2,6-diaminopurine None MR X-RAY DIFFRACTION 2.15 Å 2006 J Mol Biol
Guanine 2G9C 67 Modified pyrimidines Specifically bind the purine riboswitch None MR X-RAY DIFFRACTION 1.70 Å 2006 J Am Chem Soc
Guanine 2EEW 67 Guanine Riboswitch U47C mutant bound to hypoxanthine None MR X-RAY DIFFRACTION 2.25 Å 2007 Biochemistry
Guanine 2EEV 67 Guanine riboswitch U22C, A52G mutant bound to hypoxanthine None MR X-RAY DIFFRACTION 1.95 Å 2007 Biochemistry
Guanine 2EEU 67 Guanine riboswitch U22A, A52U mutant bound to hypoxanthine None MR X-RAY DIFFRACTION 1.95 Å 2007 Biochemistry
Guanine 2EET 67 Guanine Riboswitch A21G, U75C mutant bound to hypoxanthine None MR X-RAY DIFFRACTION 1.95 Å 2007 Biochemistry
Guanine 2EES 67 Guanine riboswitch A21U, U75A mutant bound to hypoxanthine None MR X-RAY DIFFRACTION 1.75 Å 2007 Biochemistry
Guanine 3GOT 67 Guanine riboswitch C74U mutant bound to 2-fluoroadenine. None MR X-RAY DIFFRACTION 1.95 Å 2009 Structure
Guanine 3GOG 67 Guanine riboswitch A21G,U75C mutant bound to 6-chloroguanine None MR X-RAY DIFFRACTION 2.10 Å 2009 Structure
Guanine 3GES 67 Crystal structure of the guanine riboswitch C74U mutant bound to 6-O-methylguanine None MR X-RAY DIFFRACTION 2.15 Å 2009 Structure
Guanine 3GER 67 Guanine riboswitch bound to 6-chloroguanine None MR X-RAY DIFFRACTION 1.70 Å 2009 Structure
Guanine 3GAO 67 Crystal structure of the guanine riboswitch bound to xanthine. None MR X-RAY DIFFRACTION 1.90 Å 2009 Structure
Guanine 3G4M 67 Crystal structure of guanine riboswitch bound to 2-aminopurine None MR X-RAY DIFFRACTION 2.40 Å 2009 Structure
Guanine 3FO6 68 Crystal structure of guanine riboswitch bound to 6-O-methylguanine None MR X-RAY DIFFRACTION 1.90 Å 2009 Structure
Guanine 3FO4 68 Crystal structure of guanine riboswitch C74U mutant bound to 6-chloroguanine None MR X-RAY DIFFRACTION 1.90 Å 2009 Structure
Guanine 3DS7 67 Structure of an RNA-2'-deoxyguanosine complex None MR X-RAY DIFFRACTION 1.85 Å 2009 J Mol Biol
Guanine 3RKF 67 Crystal structure of guanine riboswitch C61U/G37A double mutant bound to thio-guanine None MR X-RAY DIFFRACTION 2.50 Å 2011 Nucleic Acids Res
Guanine 2XNW 67 XPT-PBUX C74U RIBOSWITCH FROM B. SUBTILIS BOUND TO A TRIAZOLO- TRIAZOLE-DIAMINE LIGAND IDENTIFIED BY VIRTUAL SCREENING Bacillus subtilis MR X-RAY DIFFRACTION 1.50 Å 2011 Chem Biol
Guanine 2XNZ 67 xpt-pbuX C74U Riboswitch from B. subtilis bound to acetoguanamine identified by virtual screening Bacillus subtilis MR X-RAY DIFFRACTION 1.59 Å 2011 Chem Biol
Guanine 2XO0 67 xpt-pbuX C74U Riboswitch from B. subtilis bound to 24-diamino-1,3,5- triazine identified by virtual screening Bacillus subtilis MR X-RAY DIFFRACTION 1.70 Å 2011 Chem Biol
Guanine 2XO1 67 xpt-pbuX C74U Riboswitch from B. subtilis bound to N6-methyladenine Bacillus subtilis MR X-RAY DIFFRACTION 1.60 Å 2011 Chem Biol
Guanine 4FEP 67 Crystal structure of the A24U/U25A/A46G/C74U mutant xpt-pbuX guanine riboswitch aptamer domain in complex with 2,6-diaminopurine None MR X-RAY DIFFRACTION 1.65 Å 2013 J Mol Biol
Guanine 4FEO 67 Crystal structure of the AU25A/A46G/C74U mutant xpt-pbuX guanine riboswitch aptamer domain in complex with 2,6-diaminopurine None MR X-RAY DIFFRACTION 1.60 Å 2013 J Mol Biol
Guanine 4FEN 67 Crystal structure of the A24U/U25A/A46G mutant xpt-pbuX guanine riboswitch aptamer domain in complex with hypoxanthine None MR X-RAY DIFFRACTION 1.35 Å 2013 J Mol Biol
Guanine 4FEL 67 Crystal structure of the U25A/A46G mutant of the xpt-pbuX guanine riboswitch aptamer domain in complex with hypoxanthine None MR X-RAY DIFFRACTION 1.60 Å 2013 J Mol Biol
Guanine 4FEJ 67 Crystal structure of the A24U mutant xpt-pbuX guanine riboswitch aptamer domain in complex with hypoxanthine None MR X-RAY DIFFRACTION 1.50 Å 2013 J Mol Biol
Guanine 5C7U 67 5'-monophosphate wt Guanine Riboswitch bound to hypoxanthine. Bacillus subtilis subsp. subtilis str. 168 MR X-RAY DIFFRACTION 3.05 Å 2015 Angew Chem Int Ed Engl
Guanine 5C7W 67 5'-monophosphate Z:P Guanine Riboswitch bound to hypoxanthine. synthetic construct MR X-RAY DIFFRACTION 3.22 Å 2015 Angew Chem Int Ed Engl
Guanine 6UC9 67 Guanine riboswitch bound to O6-cyclohexylmethyl guanine Bacillus subtilis MR X-RAY DIFFRACTION 1.94 Å 2020 Molecules
Guanine 6UC7 67 Structure of guanine riboswitch bound to N2-acetyl guanine Bacillus subtilis MR X-RAY DIFFRACTION 1.80 Å 2020 Molecules
Guanine 6UBU 67 1.60 A resolution structure of the guanine riboswitch bound to guanine Bacillus subtilis MR X-RAY DIFFRACTION 1.60 Å 2020 Molecules
Guanine 6UC8 67 Guanine riboswitch bound to 8-aminoguanine Bacillus subtilis MR X-RAY DIFFRACTION 1.90 Å 2020 Molecules
PRPP (ykkc2b) 6CK4 117 G96A mutant of the PRPP riboswitch from T. mathranii bound to ppGpp Thermoanaerobacter mathranii MR X-RAY DIFFRACTION 3.10 Å 2018 eLife
PRPP (ykkc2b) 6CK5 117 PRPP riboswitch from T. mathranii bound to PRPP Thermoanaerobacter mathranii MR (5T83) X-RAY DIFFRACTION 2.49 Å 2018 eLife
PRPP (ykkc2b) 6DLQ 107 PRPP Riboswitch bound to PRPP, manganese chloride soaked structure Syntrophothermus lipocalidus DSM 12680 MR X-RAY DIFFRACTION 2.80 Å 2018 Nat Chem Biol
PRPP (ykkc2b) 6DLR 107 PRPP Riboswitch bound to PRPP, iridium-hexamine soaked structure Syntrophothermus lipocalidus DSM 12680 SAD-Ir X-RAY DIFFRACTION 2.66 Å 2018 Nat Chem Biol
PRPP (ykkc2b) 6DLS 107 PRPP Riboswitch bound to PRPP, thallium acetate soaked structure Syntrophothermus lipocalidus DSM 12680 MR X-RAY DIFFRACTION 2.88 Å 2018 Nat Chem Biol
PRPP (ykkc2b) 6DLT 107 PRPP Riboswitch bound to PRPP, native structure Syntrophothermus lipocalidus DSM 12680 MR X-RAY DIFFRACTION 2.90 Å 2018 Nat Chem Biol
PRPP (ykkc2b) 6DNR 107 PRPP Riboswitch bound to PRPP, ligand-free structure Syntrophothermus lipocalidus DSM 12680 MR X-RAY DIFFRACTION 2.90 Å 2018 Nat Chem Biol

Signaling molecules

Name PDB Length Description(PDB) Species Phase Determination Structure Determination Res(Å) Year Journal
C-AMP-GMP 4YAZ 84 3',3'-cGAMP riboswitch bound with 3',3'-cGAMP Geobacter MR (3IRW) X-RAY DIFFRACTION 2.00 Å 2015 Cell Rep
C-AMP-GMP 4YB0 83 3',3'-cGAMP riboswitch bound with c-di-GMP Geobacter MR X-RAY DIFFRACTION 2.12 Å 2015 Cell Rep
C-AMP-GMP 4YB1 91 20A Mutant c-di-GMP Vc2 Riboswitch bound with 3',3'-cGAMP Vibrio cholerae', 'Homo sapiens MR X-RAY DIFFRACTION 2.08 Å 2015 Cell Rep
ppGpp (ykkc2a) 6DMC 102 ppGpp Riboswitch bound to ppGpp, native structure Sulfobacillus acidophilus DSM 10332 MR (6DLR) X-RAY DIFFRACTION 2.20 Å 2018 Nat Chem Biol
ppGpp (ykkc2a) 6DMD 102 ppGpp Riboswitch bound to ppGpp, manganese chloride structure Sulfobacillus acidophilus DSM 10332 MR X-RAY DIFFRACTION 2.65 Å 2018 Nat Chem Biol
ppGpp (ykkc2a) 6DME 102 ppGpp Riboswitch bound to ppGpp, thallium acetate structure Sulfobacillus acidophilus DSM 10332 MR X-RAY DIFFRACTION 2.70 Å 2018 Nat Chem Biol
c-di-GMP-I 3IRW 98 Structure of a c-di-GMP riboswitch from V. cholerae Homo sapiens', 'Vibrio cholerae MAD-Ir-U1A X-RAY DIFFRACTION 2.70 Å 2009 Nat Struct Mol Biol
c-di-GMP-I 3IWN 93 Co-crystal structure of a bacterial c-di-GMP riboswitch Homo sapiens MR-U1A X-RAY DIFFRACTION 3.20 Å 2009 Nat Struct Mol Biol
c-di-GMP-I 3MUM 98 Crystal Structure of the G20A mutant c-di-GMP riboswith bound to c-di-GMP Homo sapiens MR X-RAY DIFFRACTION 2.90 Å 2010 Biochemistry
c-di-GMP-I 3MUR 98 Crystal Structure of the C92U mutant c-di-GMP riboswith bound to c-di-GMP Homo sapiens MR X-RAY DIFFRACTION 3.00 Å 2010 Biochemistry
c-di-GMP-I 3MUT 98 Crystal Structure of the G20A/C92U mutant c-di-GMP riboswith bound to c-di-GMP Homo sapiens MR X-RAY DIFFRACTION 3.00 Å 2010 Biochemistry
c-di-GMP-I 3MUV 98 Crystal Structure of the G20A/C92U mutant c-di-GMP riboswith bound to c-di-AMP Homo sapiens MR X-RAY DIFFRACTION 3.20 Å 2010 Biochemistry
c-di-GMP-I 3MXH 98 Native structure of a c-di-GMP riboswitch from V. cholerae Homo sapiens MR X-RAY DIFFRACTION 2.30 Å 2010 Biochemistry
c-di-GMP-I 3UCU 98 The c-di-GMP-I riboswitch bound to pGpG Homo sapiens MR X-RAY DIFFRACTION 2.80 Å 2012 Biochemistry
c-di-GMP-I 3UCZ 98 The c-di-GMP-I riboswitch bound to GpG Homo sapiens MR X-RAY DIFFRACTION 2.80 Å 2012 Biochemistry
c-di-GMP-I 3UD3 98 The C92U mutant c-di-GMP-I riboswitch bound to pGpA Homo sapiens MR X-RAY DIFFRACTION 3.10 Å 2012 Biochemistry
c-di-GMP-I 3UD4 98 The C92U mutant c-di-GMP-I riboswitch bound to GpA Homo sapiens MR X-RAY DIFFRACTION 2.70 Å 2012 Biochemistry
c-di-GMP-II 3Q3Z 75 Structure of a c-di-GMP-II riboswitch from C. acetobutylicum bound to c-di-GMP Clostridium acetobutylicum SAD-Ir X-RAY DIFFRACTION 2.51 Å 2011 Proc Natl Acad Sci U S A
c-di-AMP (ydaO) 4QLM 125 ydao riboswitch binding to c-di-AMP Caldanaerobacter subterraneus subsp. tengcongensis MB4 SAD-Ir X-RAY DIFFRACTION 2.72 Å 2014 Nat Chem Biol
c-di-AMP (ydaO) 4QLN 125 structure of ydao riboswitch binding with c-di-dAMP Caldanaerobacter subterraneus subsp. tengcongensis MB4 MR X-RAY DIFFRACTION 2.65 Å 2014 Nat Chem Biol
c-di-AMP (ydaO) 4W90 91 Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO Homo sapiens', 'Bacillus subtilis MR X-RAY DIFFRACTION 3.12 Å 2014 EMBO J
c-di-AMP (ydaO) 4W92 91 Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO Homo sapiens', 'Bacillus subtilis SAD-Se-U1A X-RAY DIFFRACTION 3.21 Å 2014 EMBO J
c-di-AMP (ydaO) 4QK8 122 Thermoanaerobacter pseudethanolicus c-di-AMP riboswitch None MR X-RAY DIFFRACTION 3.05 Å 2014 Nat Chem Biol
c-di-AMP (ydaO) 4QK9 124 Thermovirga lienii c-di-AMP riboswitch None MR (4QKA) X-RAY DIFFRACTION 3.05 Å 2014 Nat Chem Biol
c-di-AMP (ydaO) 4QKA 122 c-di-AMP riboswitch from Thermoanaerobacter pseudethanolicus, iridium hexamine soak None SAD-Ir X-RAY DIFFRACTION 3.20 Å 2014 Nat Chem Biol
c-di-AMP (ydaO) 6N5K 125 Structure of Human pir-miRNA-449c Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold Homo sapiens None X-RAY DIFFRACTION 3.10 Å None To be published
c-di-AMP (ydaO) 6WTR 125 Structure of Human pir-miRNA-300 Apical Loop Fused to the YdaO Riboswitch Scaffold Homo sapiens None X-RAY DIFFRACTION 3.08 Å None To be published
c-di-AMP (ydaO) 6WTL 124 Structure of Human pir-miRNA-19b-2 Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold Homo sapiens None X-RAY DIFFRACTION 2.85 Å None To be published
c-di-AMP (ydaO) 6N5N 125 Structure of Human pir-miRNA-208a Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold Homo sapiens None X-RAY DIFFRACTION 2.95 Å None To be published
c-di-AMP (ydaO) 6N5O 126 Structure of Human pir-miRNA-202 Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold Homo sapiens None X-RAY DIFFRACTION 2.71 Å None To be published
c-di-AMP (ydaO) 6N5P 127 Structure of Human pir-miRNA-340 Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold Homo sapiens None X-RAY DIFFRACTION 2.99 Å None To be published
c-di-AMP (ydaO) 6N5Q 128 Structure of Human pir-miRNA-378a Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold Homo sapiens None X-RAY DIFFRACTION 2.95 Å None To be published
c-di-AMP (ydaO) 6N5S 123 Structure of Human pir-miRNA-320b-2 Apical Loop and One-base-pair Stem Fused to the YdaO Riboswitch Scaffold Homo sapiens None X-RAY DIFFRACTION 2.80 Å None To be published
c-di-AMP (ydaO) 6N5T 126 Structure of Human pir-miRNA-378a Apical Loop Fused to the YdaO Riboswitch Scaffold Homo sapiens None X-RAY DIFFRACTION 2.79 Å None To be published
ZTP 4ZNP 73 The structure of A pfI Riboswitch Bound to ZMP synthetic construct SAD-Ir X-RAY DIFFRACTION 2.94 Å 2015 Structure
ZTP 4XW7 64 Crystal structure of the ZMP riboswitch at 2.50 angstrom Schaalia odontolytica SAD-Ir X-RAY DIFFRACTION 2.50 Å 2015 Chem Biol
ZTP 4XWF 64 Crystal structure of the ZMP riboswitch at 1.80 angstrom Schaalia odontolytica MR X-RAY DIFFRACTION 1.80 Å 2015 Chem Biol
ZTP 5BTP 75 Fusobacterium ulcerans ZTP riboswitch bound to ZMP synthetic construct SAD-Ir X-RAY DIFFRACTION 2.82 Å 2015 Nat Struct Mol Biol
ZTP 6OD9 75 Co-crystal structure of the Fusobacterium ulcerans ZTP riboswitch using an X-ray free-electron laser Fusobacterium ulcerans MR X-RAY DIFFRACTION 4.10 Å 2019 Acta Crystallogr F Struct Biol Commun
ZTP 6WZR 75 Fusibacterium ulcerans ZTP riboswitch bound to p-1-pyridinyl AICA Fusobacterium ulcerans MR X-RAY DIFFRACTION 3.20 Å 2020 Cell Chem Biol
ZTP 6WZS 75 Fusibacterium ulcerans ZTP riboswitch bound to m-1-pyridinyl AICA Fusobacterium ulcerans MR X-RAY DIFFRACTION 3.23 Å 2020 Cell Chem Biol

Elemental ions

Name PDB Length Description(PDB) Species Phase Determination Structure Determination Res(Å) Year Journal
Fluoride 4ENB 52 Crystal structure of fluoride riboswitch, bound to Iridium Thermotoga petrophila SAD-Ir X-RAY DIFFRACTION 2.30 Å 2012 Nature
Fluoride 3VRS 52 Crystal structure of fluoride riboswitch, soaked in Mn2+ Thermotoga petrophila MR X-RAY DIFFRACTION 2.60 Å 2012 Nature
Fluoride 4EN5 52 Crystal structure of fluoride riboswitch, Tl-Acetate soaked Thermotoga petrophila MR X-RAY DIFFRACTION 2.96 Å 2012 Nature
Fluoride 4ENA 52 Crystal structure of fluoride riboswitch, soaked in Cs+ Thermotoga petrophila MR X-RAY DIFFRACTION 2.85 Å 2012 Nature
Fluoride 4ENC 52 Crystal structure of fluoride riboswitch Thermotoga petrophila MR X-RAY DIFFRACTION 2.27 Å 2012 Nature
Fluoride 5KH8 47 Solution structures of the apo state fluoride riboswitch synthetic construct None SOLUTION NMR None 2017 Nat Chem Biol
Mg2+ 2QBZ 161 Structure of the M-Box Riboswitch Aptamer Domain None SIRAS-Cs X-RAY DIFFRACTION 2.60 Å 2007 Cell
Mg2+ 3PDR 161 Crystal structure of manganese bound M-box RNA Bacillus subtilis MR X-RAY DIFFRACTION 1.85 Å 2011 J Mol Biol
Mg2+ 2LI4 32 Solution structure of a shortened antiterminator hairpin from a Mg2+ riboswitch Yersinia enterocolitica None SOLUTION NMR None None To be published
Mn2+ 4Y1I 100 Lactococcus lactis yybP-ykoY Mn riboswitch bound to Mn2+ Lactococcus lactis subsp. lactis SAD-Ir X-RAY DIFFRACTION 2.85 Å 2015 Mol Cell
Mn2+ 4Y1J 100 Lactococcus lactis yybP-ykoY Mn riboswitch A41U binding site mutant in presence of Mn2+ Lactococcus lactis subsp. lactis MR X-RAY DIFFRACTION 2.24 Å 2015 Mol Cell
Mn2+ 4Y1M 107 An Escherichia coli yybP-ykoY Mn riboswitch in the Mn2+-free state Escherichia coli MR X-RAY DIFFRACTION 3.00 Å 2015 Mol Cell
Mn2+ 6CB3 101 Crystal structure of the L.Lactis YkoY riboswitch bound to cadmium Lactococcus lactis MR X-RAY DIFFRACTION 1.89 Å 2018 Cell Chem Biol
Mn2+ 6CC1 101 Crystal structure of ykoY-alx riboswitch chimera bound to cadmium Lactococcus lactis MR X-RAY DIFFRACTION 2.54 Å 2018 Cell Chem Biol
Mn2+ 6CC3 101 Crystal structure of ykoY-mntP riboswitch chimera bound to cadmium Lactococcus lactis MR X-RAY DIFFRACTION 2.70 Å 2018 Cell Chem Biol
Mn2+ 6N2V 99 Manganese riboswitch from Xanthmonas oryzae bound to Mn(II) Xanthomonas oryzae MR X-RAY DIFFRACTION 2.85 Å 2019 Nat Commun
NiCo 4RUM 94 Crystal structure of the NiCo transition-metal riboswitch bound to cobalt synthetic construct SAD-Co X-RAY DIFFRACTION 2.64 Å 2015 Mol Cell

Amino acids

Name PDB Length Description(PDB) Species Phase Determination Structure Determination Res(Å) Year Journal
Glycine 3OWZ 88 Crystal structure of glycine riboswitch, soaked in Iridium None MAD-Ir X-RAY DIFFRACTION 2.95 Å 2010 Mol Cell
Glycine 3OWI 88 Crystal structure of the glycine riboswitch bound to glycine Vibrio cholerae MJ-1236 MR X-RAY DIFFRACTION 2.85 Å 2010 Mol Cell
Glycine 3OWW 88 Crystal structure of the glycine riboswitch bound to glycine None MR X-RAY DIFFRACTION 2.80 Å 2010 Mol Cell
Glycine 3OX0 88 Crystal structure of glycine riboswitch, unbound state None MR X-RAY DIFFRACTION 3.05 Å 2010 Mol Cell
Glycine 3OXB 88 Crystal structure of glycine riboswitch with single mutation None MR X-RAY DIFFRACTION 2.95 Å 2010 Mol Cell
Glycine 3OXD 88 Crystal structure of glycine riboswitch with two mutations None MR X-RAY DIFFRACTION 3.00 Å 2010 Mol Cell
Glycine 3OXE 88 crystal structure of glycine riboswitch, Mn2+ soaked None MR X-RAY DIFFRACTION 2.90 Å 2010 Mol Cell
Glycine 3OXJ 88 crystal structure of glycine riboswitch, soaked in Ba2+ None MR X-RAY DIFFRACTION 3.20 Å 2010 Mol Cell
Glycine 3OXM 88 crystal structure of glycine riboswitch, Tl-Acetate soaked None MR X-RAY DIFFRACTION 2.95 Å 2010 Mol Cell
Glycine 3P49 169 Crystal Structure of a Glycine Riboswitch from Fusobacterium nucleatum Fusobacterium nucleatum subsp. polymorphum', 'Homo sapiens MR X-RAY DIFFRACTION 3.55 Å 2011 Chem Biol
Lysine 3D0U 161 Crystal Structure of Lysine Riboswitch Bound to Lysine None SAD-Ir X-RAY DIFFRACTION 2.80 Å 2008 J Biol Chem
Lysine 3D0X 161 Crystal Structure of the unbound lysine riboswitch None MR X-RAY DIFFRACTION 2.95 Å 2008 J Biol Chem
Lysine 3DIO 174 Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine, IRIDIUM HEXAMINE SOAK None MAD-Ir X-RAY DIFFRACTION 2.40 Å 2008 Nature
Lysine 3DIG 174 CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA LYSINE RIBOSWITCH BOUND TO S-(2-aminoethyl)-L-cysteine None MR X-RAY DIFFRACTION 2.80 Å 2008 Nature
Lysine 3DIL 174 Crystal structure of the Thermotoga maritima lysine riboswitch bound to lysine None MR X-RAY DIFFRACTION 1.90 Å 2008 Nature
Lysine 3DIM 174 Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine, Cs+ Soak None MR X-RAY DIFFRACTION 2.90 Å 2008 Nature
Lysine 3DIQ 174 Crystallization of the Thermotoga maritima lysine riboswitch bound to homoarginine None MR X-RAY DIFFRACTION 2.70 Å 2008 Nature
Lysine 3DIR 174 Crystallization of the Thermotoga maritima lysine riboswitch bound to N6-1-iminoethyl-L-Lysine None MR X-RAY DIFFRACTION 2.90 Å 2008 Nature
Lysine 3DIS 174 Crystallization of the Thermotoga maritima lysine riboswitch in free form None MR X-RAY DIFFRACTION 3.10 Å 2008 Nature
Lysine 3DIX 174 Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine, K+ anomalous data None MR X-RAY DIFFRACTION 2.90 Å 2008 Nature
Lysine 3DIY 174 Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine, Mn2+ soak None MR X-RAY DIFFRACTION 2.71 Å 2008 Nature
Lysine 3DIZ 174 Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine in the Absence of Mg2+ None MR X-RAY DIFFRACTION 2.85 Å 2008 Nature
Lysine 3DJ0 174 Crystallization of the Thermotoga maritima lysine riboswitch bound to L-4-oxalysine None MR X-RAY DIFFRACTION 2.50 Å 2008 Nature
Lysine 3DJ2 174 Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine, Tl+ Soak None MR X-RAY DIFFRACTION 2.50 Å 2008 Nature
Lysine 4ERJ 161 Crystal structure of the lysine riboswitch bound to a 6-aminocaproic acid Thermotoga maritima MR X-RAY DIFFRACTION 3.00 Å 2012 J Mol Biol
Lysine 4ERL 161 Crystal structure of the lysine riboswitch bound to a lysine-glycine dipeptide Thermotoga maritima MR X-RAY DIFFRACTION 3.00 Å 2012 J Mol Biol
Glutamine-I 5DDO 61 Structural and Dynamic Basis for Low Affinity-High Selectivity Binding of L-glutamine by the Gln-riboswitch Synechococcus elongatus', 'Homo sapiens MR X-RAY DIFFRACTION 3.10 Å 2015 Cell Rep
Glutamine-I 5DDP 61 L-glutamine riboswitch bound with L-glutamine Synechococcus elongatus', 'Homo sapiens MR-U1A X-RAY DIFFRACTION 2.30 Å 2015 Cell Rep
Glutamine-I 5DDQ 61 L-glutamine riboswitch bound with L-glutamine soaked with Mn2+ Synechococcus elongatus', 'Homo sapiens MR X-RAY DIFFRACTION 2.40 Å 2015 Cell Rep
Glutamine-I 5DDR 61 L-glutamine riboswitch bound with L-glutamine soaked with Cs+ Synechococcus elongatus', 'Homo sapiens MR X-RAY DIFFRACTION 2.60 Å 2015 Cell Rep
Glutamine-II 6QN3 50 Structure of the Glutamine II Riboswitch Prochlorococcus sp. MR (Homology modeling) X-RAY DIFFRACTION 2.30 Å 2019 Nucleic Acids Res

Sugars

Name PDB Length Description(PDB) Species Phase Determination Structure Determination Res(Å) Year Journal
GlcN6P 2GCS 125 Pre-cleavage state of the Thermoanaerobacter tengcongensis glmS ribozyme None MR X-RAY DIFFRACTION 2.10 Å 2006 Science
GlcN6P 2GCV 26 Post-cleavage state of the Thermoanaerobacter tengcongensis glmS ribozyme None MR X-RAY DIFFRACTION 2.10 Å 2006 Science
GlcN6P 2H0S 28 Pre-cleavage state of the Thermoanaerobacter tengcongensis glmS ribozyme None MR X-RAY DIFFRACTION 2.35 Å 2006 Science
GlcN6P 2H0W 26 Post-cleavage state of the Thermoanaerobacter tengcongensis glmS ribozyme None MR X-RAY DIFFRACTION 2.40 Å 2006 Science
GlcN6P 2H0X 27 Pre-cleavage state of the Thermoanaerobacter tengcongensis glmS ribozyme None MR X-RAY DIFFRACTION 2.30 Å 2006 Science
GlcN6P 2H0Z 27 Pre-cleavage state of the Thermoanaerobacter tengcongensis glmS ribozyme bound to glucose-6-phosphate None MR X-RAY DIFFRACTION 2.70 Å 2006 Science
GlcN6P 2HO6 27 Post-cleavage state of the Thermoanaerobacter tengcongensis glmS ribozyme None MR X-RAY DIFFRACTION 2.80 Å 2006 Science
GlcN6P 2HO7 27 Pre-cleavage state of the Thermoanaerobacter tengcongensis glmS ribozyme bound to glucose-6-phosphate None MIRAS-Os, I X-RAY DIFFRACTION 2.90 Å 2006 Science
GlcN6P 2NZ4 13 Structural investigation of the GlmS ribozyme bound to its catalytic cofactor Homo sapiens MIRAS-Ir, Co, I X-RAY DIFFRACTION 2.50 Å 2007 Chem Biol
GlcN6P 2Z74 27 T. tengcongensis glmS ribozyme bound to glucose-6-phosphate None MR X-RAY DIFFRACTION 2.20 Å 2007 J Mol Biol
GlcN6P 2Z75 27 T. tengcongensis glmS ribozyme bound to glucosamine-6-phosphate Caldanaerobacter subterraneus subsp. tengcongensis MB4 MR X-RAY DIFFRACTION 1.70 Å 2007 J Mol Biol
GlcN6P 3B4A 28 T. tengcongensis glmS ribozyme with G40A mutation, bound to glucosamine-6-phosphate Caldanaerobacter subterraneus subsp. tengcongensis MR X-RAY DIFFRACTION 2.70 Å 2007 J Am Chem Soc
GlcN6P 3B4B 26 T. tengcongensis glmS ribozyme with G40A mutation, bound to glucosamine-6-phosphate and a substrate RNA with a 2'5'-phosphodiester linkage Caldanaerobacter subterraneus subsp. tengcongensis MR X-RAY DIFFRACTION 2.70 Å 2007 J Am Chem Soc
GlcN6P 3B4C 26 T. tengcongensis glmS ribozyme bound to glucosamine-6-phosphate and a substrate RNA with a 2'5'-phosphodiester linkage Caldanaerobacter subterraneus subsp. tengcongensis MR X-RAY DIFFRACTION 3.00 Å 2007 J Am Chem Soc
GlcN6P 3G8S 98 Crystal structure of the pre-cleaved Bacillus anthracis glmS ribozyme Homo sapiens MR X-RAY DIFFRACTION 3.10 Å 2009 Biochemistry
GlcN6P 3G8T 98 Crystal structure of the G33A mutant Bacillus anthracis glmS ribozyme bound to GlcN6P Homo sapiens', 'synthetic construct MR X-RAY DIFFRACTION 3.00 Å 2009 Biochemistry
GlcN6P 3G96 98 Crystal structure of the Bacillus anthracis glmS ribozyme bound to MaN6P Homo sapiens', 'synthetic construct MR X-RAY DIFFRACTION 3.01 Å 2009 Biochemistry
GlcN6P 3G9C 98 Crystal structure of the product Bacillus anthracis glmS ribozyme Homo sapiens', 'synthetic construct MR X-RAY DIFFRACTION 2.90 Å 2009 Biochemistry
GlcN6P 3L3C 90 Crystal structure of the Bacillus anthracis glmS ribozyme bound to Glc6P Homo sapiens MR X-RAY DIFFRACTION 2.85 Å 2009 Biochemistry
GlcN6P 4MEG 27 In vitro evolved glmS ribozyme triple mutant, magnesium ion complex None MR X-RAY DIFFRACTION 3.10 Å 2013 Nat Chem Biol
GlcN6P 4MEH 27 In vitro evolved glmS ribozyme triple mutant, calcium ion complex None MR X-RAY DIFFRACTION 3.12 Å 2013 Nat Chem Biol

T-box

Name PDB Length Description(PDB) Species Phase Determination Structure Determination Res(Å) Year Journal
T-box 6PMO 66 and 75 Co-crystal structure of the Geobacillus kaustophilus glyQ T-box riboswitch discriminator domain in complex with tRNA-Gly Geobacillus kaustophilus SAD-Ir X-RAY DIFFRACTION 2.66 Å 2019 NSMB
T-box 6POM 169 and 75 Cryo-EM structure of the full-length Bacillus subtilis glyQS T-box riboswitch in complex with tRNA-Gly Bacillus subtilis Cryo-EM ELECTRON MICROSCOPY 4.90 Å 2019 NSMB
T-box 6UFM 98 and 77 Cocrystal Structure of the Nocardia farcinica ileS T-box riboswitch in complex with its cognate tRNA Mycolicibacterium smegmatis', 'Nocardia farcinica SAD-Ir X-RAY DIFFRACTION 2.82 Å 2019 NSMB
T-box 7UQ6 86 tRNA T-box antiterminator fusion, construct #4 Geobacillus kaustophilus MR X-RAY DIFFRACTION 2.95 Å None To be published
T-box 7UZ0 87 AntiT-tRNA flip UCCA Geobacillus kaustophilus MR X-RAY DIFFRACTION 3.03 Å None To be published
T-box 4LCK 102 and 75 Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA Bacillus subtilis subsp. subtilis str. 168, Oceanobacillus iheyensis SAD-Se, Sr MR (Fragments) X-RAY DIFFRACTION 3.20 Å 2013 Nature
T-box 4MGN 86 and 75 Co-crystal structure of the G. kaustophilus glyQS T box riboswitch Stem I in complex with tRNA Geobacillus kaustophilus MR, SAD-Ba X-RAY DIFFRACTION 3.21 Å 2013 Structure
T-box 6UFG 166 and 77 Co-crystal structure of M. tuberculosis ileS T-box in complex with tRNA-3'-OH Mycobacterium tuberculosis SAD-Ir, MR X-RAY DIFFRACTION 2.93 Å 2019 NSMB
T-box 6UFH 167 and 77 Co-crystal structure of M. tuberculosis ileS T-box in complex with tRNA-3'-2'3'cyclic phosphate Mycobacterium tuberculosis MR X-RAY DIFFRACTION 3.10 Å 2019 NSMB
T-box 4TZP 102 and 75 As Grown, Untreated Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its cognate tRNAGly, and B. subtilis YbxF protein Bacillus subtilis, Oceanobacillus iheyensis MR X-RAY DIFFRACTION 8.50 Å 2014 Structure
T-box 4TZV 102 and 75 Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly, and B. subtilis YbxF protein, treated by removing lithium sulfate post crystallization Bacillus subtilis, Oceanobacillus iheyensis HTE831 MR X-RAY DIFFRACTION 5.03 Å 2014 Structure
T-box 4TZW 102 and 75 Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly, and B. subtilis YbxF protein, treated by removing lithium sulfate and replacing Mg2+ with Sr2+ post crystallization Bacillus subtilis, Oceanobacillus iheyensis HTE831 MR X-RAY DIFFRACTION 4.67 Å 2014 Structure
T-box 4TZZ 102 and 75 Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly, and B. subtilis YbxF protein, treated by removing lithium sulfate and increasing PEG3350 concentration from 20% to 45% post crystallization Bacillus subtilis, Oceanobacillus iheyensis MR X-RAY DIFFRACTION 3.64 Å 2014 Structure

Others

Name PDB Length Description(PDB) Species Phase Determination Structure Determination Res(Å) Year Journal
Guanidine-I 5T83 95 Structure of a guanidine-I riboswitch from S. acidophilus Sulfobacillus acidophilus DSM 10332 MAD-Ir / SIRAS X-RAY DIFFRACTION 2.71 Å 2017 Structure
Guanidine-I 5U3G 85 Structure of the Dickeya dadantii ykkC riboswitch bound to guanidinium Dickeya dadantii SAD-Ir X-RAY DIFFRACTION 2.30 Å 2017 RNA
Guanidine-I 7MLW 128 Burkholderia sp. TJI49 Guanidine-I riboswitch Burkholderia sp. TJI49 MR (5T83) X-RAY DIFFRACTION 2.70 Å 2021 RNA
Guanidine-II P2-6bp 5NDH 16 The structure of the G. violaceus guanidine II riboswitch P2 stem-loop Gloeobacter violaceus SAD-Br X-RAY DIFFRACTION 1.81 Å 2017 Cell Chem Biol
Guanidine-II P1-8bp 5NDI 20 The structure of the E.coli guanidine II riboswitch P1 stem-loop Escherichia coli SAD-Br X-RAY DIFFRACTION 2.57 Å 2017 Cell Chem Biol
Guanidine-II P1-7bp 5NEO 18 The structure of the G. violaceus guanidine II riboswitch P1 stem-loop Gloeobacter violaceus SAD-Br X-RAY DIFFRACTION 1.69 Å 2017 Cell Chem Biol
Guanidine-II P1-7bp 5NEF 18 The structure of the G. violaceus guanidine II riboswitch P1 stem-loop with guanidine Gloeobacter violaceus MR X-RAY DIFFRACTION 1.91 Å 2017 Cell Chem Biol
Guanidine-II P1-7bp 5NEP 18 The structure of the G. violaceus guanidine II riboswitch P1 stem-loop with methylguanidine Gloeobacter violaceus MR X-RAY DIFFRACTION 1.60 Å 2017 Cell Chem Biol
Guanidine-II P1-7bp 5NEQ 18 The structure of the G. violaceus guanidine II riboswitch P1 stem-loop with aminoguanidine Gloeobacter violaceus MR X-RAY DIFFRACTION 1.69 Å 2017 Cell Chem Biol
Guanidine-II P1-7bp 5NEX 18 The structure of the G. violaceus guanidine II riboswitch P1 stem-loop with agmatine Gloeobacter violaceus MR X-RAY DIFFRACTION 1.72 Å 2017 Cell Chem Biol
Guanidine-II P1-7bp 5NOM 18 The structure of the G. violaceus guanidine II riboswitch P1 stem-loop with guanidine Gloeobacter violaceus MR X-RAY DIFFRACTION 1.93 Å 2017 Cell Chem Biol
Guanidine-II P2-6bp 5VJB 16 Guanidine-II riboswitch P2 hairpin dimer with 5-bromoU substitution from Pseudomonas aeruginosa Pseudomonas aeruginosa SAD-Br X-RAY DIFFRACTION 2.10 Å 2017 RNA
Guanidine-II P2-6bp 5VJ9 16 Guanidine-II riboswitch P2 hairpin dimer from Pseudomonas aeruginosa Pseudomonas aeruginosa MR X-RAY DIFFRACTION 1.57 Å 2017 RNA
Guanidine-II P2-7bp 6HBT 18 The structure of the G. violaceus guanidine II riboswitch P2 stem-loop with arcaine Gloeobacter violaceus MR X-RAY DIFFRACTION 1.66 Å 2019 RNA
Guanidine-II P2-7bp 6HBX 18 The structure of the G. violaceus guanidine II riboswitch P2 stem-loop with ethylguanidine Gloeobacter violaceus MR X-RAY DIFFRACTION 1.54 Å 2019 RNA
Guanidine-II P2-7bp 6HC5 18 The structure of the G. violaceus guanidine II riboswitch P2 stem-loop with audouine Gloeobacter violaceus MR X-RAY DIFFRACTION 1.41 Å 2019 RNA
Guanidine-III 5NWQ 41 The structure of the thermobifida fusca guanidine III riboswitch with guanidine. Thermobifida fusca SAD-Br X-RAY DIFFRACTION 1.91 Å 2017 Cell Chem Biol
Guanidine-III 5NY8 41 The structure of the thermobifida fusca guanidine III riboswitch with aminoguanidine Thermobifida fusca MR X-RAY DIFFRACTION 2.04 Å 2017 Cell Chem Biol
Guanidine-III 5NZ3 41 The structure of the thermobifida fusca guanidine III riboswitch with methylguanidine Thermobifida fusca MR X-RAY DIFFRACTION 2.06 Å 2017 Cell Chem Biol
Guanidine-III 5NZ6 41 The structure of the thermobifida fusca guanidine III riboswitch with guanidine in space group P3212. Thermobifida fusca MR X-RAY DIFFRACTION 2.94 Å 2017 Cell Chem Biol
Guanidine-III 5NZD 41 The structure of the thermobifida fusca guanidine III riboswitch in space group P212121. Thermobifida fusca MR X-RAY DIFFRACTION 2.01 Å 2017 Cell Chem Biol
Guanidine-III 5O62 41 The structure of the thermobifida fusca guanidine III riboswitch with 1-Ethylguanidine. Thermobifida fusca MR X-RAY DIFFRACTION 2.12 Å 2017 Cell Chem Biol
Guanidine-III 5O69 41 The structure of the thermobifida fusca guanidine III riboswitch with agmatine. Thermobifida fusca MR X-RAY DIFFRACTION 2.32 Å 2017 Cell Chem Biol