Riboswitch 3D structures: Difference between revisions

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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#tree:id=OrganizedByTopic|openlevels=0|
{{#tree:id=OrganizedByTopic|openlevels=0|
*Adenine riboswitch
*Adenine riboswitch
**[[1y26]], [[4tzx]], [[4tzy]], [[4xnr]], [[5swd]], [[5swe]], [[5uza]], [[6vwt]], [[6vwv]] – VvAR + adenine – ''Vibrio vulnificus''<br />
**[[1y26]], [[4tzx]], [[4tzy]], [[4xnr]], [[5swd]], [[5swe]], [[5uza]], [[6vwt]], [[6vwv]] – VvAR + adenine – ''Vibrio vulnificus''<br />
**[[5e54]] – VvAR <br />
**[[5e54]] – VvAR <br />
**[[3ivn]] – BsAR (mutant) – ''Bacillus subtilis''<br />
**[[3ivn]] – BsAR (mutant) – ''Bacillus subtilis''<br />
**[[3la5]] - BsAR (mutant) + azacytosine<br />
**[[3la5]] - BsAR (mutant) + azacytosine<br />
*Guanine riboswitch
*Guanine riboswitch
**[[1y27]] – BsGR residues 185-252 + guanine<br />  
**[[1y27]] – BsGR residues 185-252 + guanine<br />  
**[[2g9c]], [[3fo4]], [[3fo6]], [[3ges]], [[3gog]], [[3rkf]] - BsGR (mutant) + guanine derivative<br />
**[[2g9c]], [[3fo4]], [[3fo6]], [[3ges]], [[3gog]], [[3rkf]] - BsGR (mutant) + guanine derivative<br />
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**[[6p2h]] – sGR <br />
**[[6p2h]] – sGR <br />
**[[2b57]] – GR + purine derivative<br />
**[[2b57]] – GR + purine derivative<br />
*Guanidine riboswitch
*Guanidine riboswitch
**[[5nwq]], [[5ny8]], [[5nz3]], [[5nz6]], [[5o62]] – TfGNR + guanidine derivative – ''Thermobifida fusca''<br />
**[[5nwq]], [[5ny8]], [[5nz3]], [[5nz6]], [[5o62]] – TfGNR + guanidine derivative – ''Thermobifida fusca''<br />
**[[5o69]] – TfGNR + agmatine <br />
**[[5o69]] – TfGNR + agmatine <br />
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**[[5ndh]], [[5ndi]], [[5nef]], [[5neo]], [[5nep]], [[5neq]], [[5nex]], [[5nom]] – GNR + guanidine derivative – ''Gloeobacter violaceus'' <br />
**[[5ndh]], [[5ndi]], [[5nef]], [[5neo]], [[5nep]], [[5neq]], [[5nex]], [[5nom]] – GNR + guanidine derivative – ''Gloeobacter violaceus'' <br />
**[[5vj9]], [[5vjb]] – GNR + guanidine – ''Pseudomonas aeruginosa'' <br />
**[[5vj9]], [[5vjb]] – GNR + guanidine – ''Pseudomonas aeruginosa'' <br />
*Xanthine riboswitch
*Xanthine riboswitch
**[[7elp]], [[7elq]], [[7elr]], [[7els]] – XR + xanthine derivative – ''Ideonella''<br />
**[[7elp]], [[7elq]], [[7elr]], [[7els]] – XR + xanthine derivative – ''Ideonella''<br />
*Thiamine pyrophosphate riboswitch
*Thiamine pyrophosphate riboswitch
**[[2gdi]] – TPPR + TPP – synthetic
**[[2gdi]] – TPPR + TPP – synthetic
**[[2hoj]], [[2hok]], [[2hol]] – EcTPPR + TPP + metal ion – ''Escherichia coli''
**[[2hoj]], [[2hok]], [[2hol]] – EcTPPR + TPP + metal ion – ''Escherichia coli''
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**[[4nyg]], [[7td7]], [[7tda]], [[7tdb]] – EcTPPR + thiamine derivative<br />
**[[4nyg]], [[7td7]], [[7tda]], [[7tdb]] – EcTPPR + thiamine derivative<br />
**[[2cky]], [[3d2g]], [[3d2v]], [[3d2x]] - TPPR + TPP analog – ''Arabidopsis thaliana''
**[[2cky]], [[3d2g]], [[3d2v]], [[3d2x]] - TPPR + TPP analog – ''Arabidopsis thaliana''
*S-adenosylmethionine riboswitch or SAM riboswitch
*S-adenosylmethionine riboswitch or SAM riboswitch
**[[2gis]], [[4aob]], [[4b5r]], [[4l81]] – TtSAMR + SAM – ''Thermoanaerobacter tengcongensis''
**[[2gis]], [[4aob]], [[4b5r]], [[4l81]] – TtSAMR + SAM – ''Thermoanaerobacter tengcongensis''
**[[3iqr]], [[2ydh]], [[2ygh]] - TtSAMR (mutant) + SAM
**[[3iqr]], [[2ydh]], [[2ygh]] - TtSAMR (mutant) + SAM
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S-adenosylhomocysteine riboswitch or SAH riboswitch
S-adenosylhomocysteine riboswitch or SAH riboswitch
**[[3npn]], [[3npq]] – SAHR + SAH – ''Ralstonia solanacearum''
**[[3npn]], [[3npq]] – SAHR + SAH – ''Ralstonia solanacearum''
**[[6hag]] - SAMR + SAH – ''proteobacteria'' - NMR<br />
**[[6hag]] - SAMR + SAH – ''proteobacteria'' - NMR<br />
*SAM/SAH riboswitch
*SAM/SAH riboswitch
**[[6ymk]] – RoSAM/SAH + adenosine derivative + cytidine derivative – ''Roseobacter''<br />
**[[6ymk]] – RoSAM/SAH + adenosine derivative + cytidine derivative – ''Roseobacter''<br />
**[[6ylb]], [[6ymm]] – RoSAM/SAH + SAM<br />
**[[6ylb]], [[6ymm]] – RoSAM/SAH + SAM<br />
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**[[7d7w]], [[7d7x]], [[7d7z]], [[7d81]], [[7d82]] – AbNADR + NAD - ''Acidobacteriaceae bacterium''<br />
**[[7d7w]], [[7d7x]], [[7d7z]], [[7d81]], [[7d82]] – AbNADR + NAD - ''Acidobacteriaceae bacterium''<br />
**[[7d7v]] – AbNADR + NAD + U1 small nuclear ribonucleoprotein<br />
**[[7d7v]] – AbNADR + NAD + U1 small nuclear ribonucleoprotein<br />
*Lysine riboswitch
*Lysine riboswitch
**[[3d0u]] – TmKR ligand-binding domain + Lysine – ''Thermotoga maritime''
**[[3d0u]] – TmKR ligand-binding domain + Lysine – ''Thermotoga maritime''
**[[4erj]] – TmKR + aminocaproic acid<br />
**[[4erj]] – TmKR + aminocaproic acid<br />
**[[4erl]] – TmKR + Lys + Gly<br />
**[[4erl]] – TmKR + Lys + Gly<br />
*FMN riboswitch
*FMN riboswitch
**[[6wjr]], [[6wjs]] - FnFMNR – ''Fusobacterium nucleatum''<br />
**[[6wjr]], [[6wjs]] - FnFMNR – ''Fusobacterium nucleatum''<br />
**[[3f2q]], [[3f2t]], [[3f2w]], [[3f2x]], [[3f2y]], [[3f30]], [[3f4e]] – FnFMNR + FMN
**[[3f2q]], [[3f2t]], [[3f2w]], [[3f2x]], [[3f2y]], [[3f30]], [[3f4e]] – FnFMNR + FMN
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**[[2yif]] - FnFMNR + GTP
**[[2yif]] - FnFMNR + GTP
**[[6bfb]] – FnFMNR + inhibitor<br />
**[[6bfb]] – FnFMNR + inhibitor<br />
*Pre-queosine riboswitch
*Pre-queosine riboswitch
**[[3fu2]], [[3k1v]] – BsPreq1R + queosine
**[[3fu2]], [[3k1v]] – BsPreq1R + queosine
**[[3gca]] – TtPreq1R + queosine
**[[3gca]] – TtPreq1R + queosine
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**[[4qk8]], [[4qka]] – GMPR + GTP – ''Thermoanaerobacter pseudethanolicus''<br />
**[[4qk8]], [[4qka]] – GMPR + GTP – ''Thermoanaerobacter pseudethanolicus''<br />
**[[4qk9]] – GMPR + guanosine derivative – ''Thermovirga lienii''<br />
**[[4qk9]] – GMPR + guanosine derivative – ''Thermovirga lienii''<br />
*Glycine riboswitch
*Glycine riboswitch
**[[6wlt]], [[6wlu]] – VcGlyR<br />
**[[6wlt]], [[6wlu]] – VcGlyR<br />
**[[3owi]], [[3oww]], [[3owz]] – VcGlyR + glycine
**[[3owi]], [[3oww]], [[3owz]] – VcGlyR + glycine
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**[[6wll]], [[6wlm]] – FnGlyR<br />
**[[6wll]], [[6wlm]] – FnGlyR<br />
**[[3p49]] – FnGlyR + U1 small nuclear ribonucleoprotein + glycine
**[[3p49]] – FnGlyR + U1 small nuclear ribonucleoprotein + glycine
*Glutamine riboswitch
*Glutamine riboswitch
**[[6qn3]] – GlnR II + Gln – ''Prochlorococcus''<br />
**[[6qn3]] – GlnR II + Gln – ''Prochlorococcus''<br />
*M-Box riboswitch
*M-Box riboswitch
**[[3pdr]] – BsMBR + Mn
**[[3pdr]] – BsMBR + Mn
*T-Box riboswitch
*T-Box riboswitch
**[[4lck]] – sTBR + tRNA-Gly + ribosomal protein YBXF – synthetic<br />
**[[4lck]] – sTBR + tRNA-Gly + ribosomal protein YBXF – synthetic<br />
**[[4mgn]] – sTBR + tRNA-Gly <br />
**[[4mgn]] – sTBR + tRNA-Gly <br />
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**[[6ufg]], [[6ufh]] – MtTBR + tRNA <br />
**[[6ufg]], [[6ufh]] – MtTBR + tRNA <br />
**[[6pom]] – BsTBR + tRNA-Gly – Cryo EM<br />
**[[6pom]] – BsTBR + tRNA-Gly – Cryo EM<br />
*Tetrahydrofolate riboswitch
*Tetrahydrofolate riboswitch
**[[3suh]], [[3sux]] – EsTHFR + THF derivative – Eubacterium siraeum
**[[3suh]], [[3sux]] – EsTHFR + THF derivative – Eubacterium siraeum
**[[3suy]] - EsTHFR + cytidine cyclic phosphate
**[[3suy]] - EsTHFR + cytidine cyclic phosphate
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[[4ena]] – TpFR + Mg + Cs + GTP + F <br />
[[4ena]] – TpFR + Mg + Cs + GTP + F <br />
[[4enb]] – TpFR + Mg + Ir + K + GTP + F <br />
[[4enb]] – TpFR + Mg + Ir + K + GTP + F <br />
*Manganese riboswitch
*Manganese riboswitch
**[[6n2v]] – MnR + Mn – ''Xanthomonas oryzae''<br />
**[[6n2v]] – MnR + Mn – ''Xanthomonas oryzae''<br />
*Cobalamine riboswitch
*Cobalamine riboswitch


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**[[6vmy]], [[8fw4]] – BsCoR <br />
**[[6vmy]], [[8fw4]] – BsCoR <br />
**[[8sa2]], [[8sa3]], [[8sa4]], [[8sa5]], [[8sa6]] – BsCoR – Cryo EM<br />
**[[8sa2]], [[8sa3]], [[8sa4]], [[8sa5]], [[8sa6]] – BsCoR – Cryo EM<br />
*YdaO riboswitch
*YdaO riboswitch
**[[6n5k]], [[6n5n]], [[6n5o]], [[6n5p]], [[6n5q]], [[6n5s]], [[6n5t]], [[6wtl]], [[6wtr]] – hYdaO/mRNA <br />
**[[6n5k]], [[6n5n]], [[6n5o]], [[6n5p]], [[6n5q]], [[6n5s]], [[6n5t]], [[6wtl]], [[6wtr]] – hYdaO/mRNA <br />


* yybp-ykoy riboswitch
* yybp-ykoy riboswitch
**[[4y1i]] – LlYYR + Mn – ''Lactobacillus lactis''<br />
**[[4y1i]] – LlYYR + Mn – ''Lactobacillus lactis''<br />
**[[4y1j]] – LlYYR (mutant) + Mn<br />
**[[4y1j]] – LlYYR (mutant) + Mn<br />
**[[6cb3]], [[6cc1]], [[6cc3]] – LlYYR + GTP<br />
**[[6cb3]], [[6cc1]], [[6cc3]] – LlYYR + GTP<br />
**[[4y1m]] – EcYYR <br />
**[[4y1m]] – EcYYR <br />
* PRPP riboswitch
* PRPP riboswitch
**[[6dnr]] – SlPRPPR + GTP + cytidine phosphate – ''Syntrophothermus lipocalidus''<br />
**[[6dnr]] – SlPRPPR + GTP + cytidine phosphate – ''Syntrophothermus lipocalidus''<br />
**[[6dlq]], [[6dls]], [[6dlt]] – SlPRPPR + GTP + cytidine phosphate + PRP<br />
**[[6dlq]], [[6dls]], [[6dlt]] – SlPRPPR + GTP + cytidine phosphate + PRP<br />
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**[[6ck5]] – TmPRPPR + PRPP – ''Thermoanaerobacter mathranii''<br />
**[[6ck5]] – TmPRPPR + PRPP – ''Thermoanaerobacter mathranii''<br />
**[[6ck4]] – TmPRPPR (mutant) + G4P<br />
**[[6ck4]] – TmPRPPR (mutant) + G4P<br />
* PPGPP riboswitch
* PPGPP riboswitch
**[[6dme]], [[6dmd]], [[6dmc]] – SaPPGPPR + GTP + cytidine phosphate + guanine tetraphosphate – ''Sulfobacillus acidophilus''<br />
**[[6dme]], [[6dmd]], [[6dmc]] – SaPPGPPR + GTP + cytidine phosphate + guanine tetraphosphate – ''Sulfobacillus acidophilus''<br />
*PFI riboswitch
*PFI riboswitch
**[[4znp]] – PFIR + AICAR – synthetic<br />
**[[4znp]] – PFIR + AICAR – synthetic<br />
*NiCo riboswitch
*NiCo riboswitch
**[[4rum]] – NiCoR + Co – synthetic<br />
**[[4rum]] – NiCoR + Co – synthetic<br />
*ZMP riboswitch
*ZMP riboswitch
**[[4xw7]], [[4xwf]] – ZMPR + AICAR – ''Actinomyces odontolyticus'' <br />
**[[4xw7]], [[4xwf]] – ZMPR + AICAR – ''Actinomyces odontolyticus'' <br />
*ZTP riboswitch
*ZTP riboswitch
**[[6od9]] – FuZTP – ''Fusobacterium ulcerans''<br />
**[[6od9]] – FuZTP – ''Fusobacterium ulcerans''<br />
**[[6wzr]], [[6wzs]] – FuZTP + pyridine derivative<br />
**[[6wzr]], [[6wzs]] – FuZTP + pyridine derivative<br />
**[[5btp]] – FuZTPR + AICAR <br />
**[[5btp]] – FuZTPR + AICAR <br />
*Deoxyguanosine riboswitch
*Deoxyguanosine riboswitch
**[[3sk4]], [[3ski]], [[3skl]], [[3skt]], [[3skz]], [[3slm]], [[3slq]] – DgR + guanosine derivative<br />
**[[3sk4]], [[3ski]], [[3skl]], [[3skt]], [[3skz]], [[3slm]], [[3slq]] – DgR + guanosine derivative<br />
*ThiM riboswitch
*ThiM riboswitch
**[[7tzr]], [[7tzs]], [[7tzt]], [[7tzu]] – EcThR + quinoxaline derivative <br />
**[[7tzr]], [[7tzs]], [[7tzt]], [[7tzu]] – EcThR + quinoxaline derivative <br />
**[[3k0j]] – EcThR + thiamine pyrophosphate  
**[[3k0j]] – EcThR + thiamine pyrophosphate  

Revision as of 09:41, 29 March 2026

3D structures of riboswitch

Updated on 29-March-2026

S-adenosylhomocysteine riboswitch or SAH riboswitch

    • 3npn, 3npq – SAHR + SAH – Ralstonia solanacearum
    • 6hag - SAMR + SAH – proteobacteria - NMR
  • SAM/SAH riboswitch
    • 6ymk – RoSAM/SAH + adenosine derivative + cytidine derivative – Roseobacter
    • 6ylb, 6ymm – RoSAM/SAH + SAM
    • 6ymi – RoSAM/SAH + AMP
    • 6yl5, 6yml – RoSAM/SAH + SAH
    • 6ymj – RoSAM/SAH + adenosine
  • NAD+ riboswitch
  • Lysine riboswitch
    • 3d0u – TmKR ligand-binding domain + Lysine – Thermotoga maritime
    • 4erj – TmKR + aminocaproic acid
    • 4erl – TmKR + Lys + Gly
  • FMN riboswitch
  • Pre-queosine riboswitch
    • 3fu2, 3k1v – BsPreq1R + queosine
    • 3gca – TtPreq1R + queosine
    • 3q50, 3q51 – TtPreq1R aptamer domain + queosine
    • 4jf2 – Preq1R + GTP + deaza-aminomethyl guanine – Lactobacillus rhamnosus
    • 6vuh, 6vui – CsPreq1
    • 6e1s, 6e1t, 6e1u, 6e1v, 6e1w, 7e9e, 7e9i – CsPreq1 + probe
    • 6xkn, 6xko – Preq1 + GTP + guanine derivative – Faecalibacterium prausnitzii
    • 7rex, 8fb3 – Preq1 + guanine derivative – Carnobacterium antarcticum
    • 2miy – Preq1 + guanine derivative – Streptococcus pneumoniae - NMR
    • 8fza – EcPreq1 III
    • 2l1v – EcPreq1 I + PreQ1 - NMR

C-di-GMP riboswitch

    • 3ucu, 3ucz – hGMPR + GpG
    • 3ud3, 3ud4 – hGMPR + GpA
    • 3irw, 3mxh – VcGMPR + C-di-GMP + GTP + U1 small nuclear ribonucleoprotein – Vibrio cholerae
    • 3iwn – VcGMPR + C-di-GMP + U1 small nuclear ribonucleoprotein
    • 3mum, 3mur, 3mut - VcGMPR (mutant) + C-di-GMP + U1 small nuclear ribonucleoprotein
    • 3muv - VcGMPR (mutant) + C-di-AMP + U1 small nuclear ribonucleoprotein
    • 3q3z - GMPR + C-di-GMP – Clostridium acetobutylicum
    • 4qk8, 4qka – GMPR + GTP – Thermoanaerobacter pseudethanolicus
    • 4qk9 – GMPR + guanosine derivative – Thermovirga lienii
  • Glycine riboswitch
  • Glutamine riboswitch
    • 6qn3 – GlnR II + Gln – Prochlorococcus
  • M-Box riboswitch
  • T-Box riboswitch
    • 4lck – sTBR + tRNA-Gly + ribosomal protein YBXF – synthetic
    • 4mgn – sTBR + tRNA-Gly
    • 6ufm – TBR + tRNA – Mycolicibacterium smegmatis
    • 6ufg, 6ufh – MtTBR + tRNA
    • 6pom – BsTBR + tRNA-Gly – Cryo EM
  • Tetrahydrofolate riboswitch
    • 3suh, 3sux – EsTHFR + THF derivative – Eubacterium siraeum
    • 3suy - EsTHFR + cytidine cyclic phosphate
    • 4lvv, 4lvx, 4lvw, 4lvy, 4lvz, 4lw0 – THFR + purine derivative – synthetic
    • 3sd3 – THFR (mutant) + pteridine derivative – synthetic 
    • 1qa4, 1qa5 – NEF anchor domain – NMR
    • 7kd1 – SmTHFR – Streptococcus mutans
    • 6q57 – SmTHFR + pterin derivative
    • 7wia, 7wib – MlTHFR – Mesorhizobium loti
    • 7wie – MlTHFR + 7DG
    • 7wii – MlTHFR + NPR
    • 7wif – MlTHFR + H4B

  Fluoride riboswitch 3vrs – TpFR + Mn + K + F – Thermotoga petrophila
4en5 – TpFR + Mg + Tl + F
4enc – TpFR + Mg + K + F
4ena – TpFR + Mg + Cs + GTP + F
4enb – TpFR + Mg + Ir + K + GTP + F

  • Manganese riboswitch
    • 6n2v – MnR + Mn – Xanthomonas oryzae
  • Cobalamine riboswitch

4frg, 4frn, 4gma, 4gxy – CoR + aptamer domain – Marine metagenome

  • YdaO riboswitch
  • yybp-ykoy riboswitch
    • 4y1i – LlYYR + Mn – Lactobacillus lactis
    • 4y1j – LlYYR (mutant) + Mn
    • 6cb3, 6cc1, 6cc3 – LlYYR + GTP
    • 4y1m – EcYYR
  • PRPP riboswitch
    • 6dnr – SlPRPPR + GTP + cytidine phosphate – Syntrophothermus lipocalidus
    • 6dlq, 6dls, 6dlt – SlPRPPR + GTP + cytidine phosphate + PRP
    • 6dlr – SlPRPPR + cytidine phosphate + PRP
    • 6ck5 – TmPRPPR + PRPP – Thermoanaerobacter mathranii
    • 6ck4 – TmPRPPR (mutant) + G4P
  • PPGPP riboswitch
    • 6dme, 6dmd, 6dmc – SaPPGPPR + GTP + cytidine phosphate + guanine tetraphosphate – Sulfobacillus acidophilus
  • PFI riboswitch
    • 4znp – PFIR + AICAR – synthetic
  • NiCo riboswitch
    • 4rum – NiCoR + Co – synthetic
  • ZMP riboswitch
    • 4xw7, 4xwf – ZMPR + AICAR – Actinomyces odontolyticus
  • ZTP riboswitch
    • 6od9 – FuZTP – Fusobacterium ulcerans
    • 6wzr, 6wzs – FuZTP + pyridine derivative
    • 5btp – FuZTPR + AICAR
  • Deoxyguanosine riboswitch
  • ThiM riboswitch

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Openfox

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