Riboswitch 3D structures: Difference between revisions

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*Adenine riboswitch
*Adenine riboswitch


**[[1y26]], [[4tzx]], [[4tzy]], [[4xnr]], [[5swd]], [[5swe]], [[5uza]] – 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 />
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**[[3gao]] - BsGR  + xanthine<br />
**[[3gao]] - BsGR  + xanthine<br />
**[[2xnw]] – BsGR + Mn<br />
**[[2xnw]] – BsGR + Mn<br />
**[[4fe5]], [[4fej]], [[4fel]], [[4fen]], [[4feo]], [[4fep]] – GR + hypoxanthine – synthetic<br />
**[[4fe5]], [[4fej]], [[4fel]], [[4fen]], [[4feo]], [[4fep]] – sGR + hypoxanthine – synthetic<br />
**[[6p2h]] – sGR <br />


*Guanidine riboswitch
*Guanidine riboswitch
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**[[5nwq]] – TfGR + guanidine – ''Thermobifida fusca''<br />
**[[5nwq]] – TfGR + guanidine – ''Thermobifida fusca''<br />
**[[5nzd]] – TfGR + CDP derivative<br />
**[[5nzd]] – TfGR + CDP derivative<br />
**[[7mlw]] – GR + guanidine – ''Burkholderia''<br />
**[[6hbt]], [[6hbx]], [[6hc5]] – GR + guanidine II + inhibitor – ''Gloeobacter violaceus''<br />
*Xanthine riboswitch
**[[7elp]], [[7elq]], [[7elr]], [[7els]] – GR + xanthine derivative – ''Ideonella''<br />


*Thiamine pyrophosphate riboswitch
*Thiamine pyrophosphate riboswitch
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**[[2hom]] – EcTPPR + TMP<br />
**[[2hom]] – EcTPPR + TMP<br />
**[[2hoo]], [[2hop]] – EcTPPR + TPP analog<br />
**[[2hoo]], [[2hop]] – EcTPPR + TPP analog<br />
**[[4nya]], [[4nyb]], [[4nyc]] – EcTPPR + pyrimidine derivative<br />
**[[4nya]], [[4nyb]], [[4nyc]], [[7tdc]] – EcTPPR + pyrimidine derivative<br />
**[[4nyd]] – EcTPPR + hypoxanthine <br />
**[[4nyd]] – EcTPPR + hypoxanthine <br />
**[[4nyg]] – EcTPPR + thyamine <br />
**[[4nyg]], [[7td7]], [[7tda]], [[7tdb]]  – EcTPPR + thiamine derivative<br />
**[[3d2g]], [[3d2v]], [[3d2x]] - TPPR + TPP analog – ''Arabidopsis thaliana''
**[[3d2g]], [[3d2v]], [[3d2x]] - TPPR + TPP analog – ''Arabidopsis thaliana''


*S-adenosylmethionine riboswitch
*S-adenosylmethionine riboswitch or SAM riboswitch


**[[2gis]], [[4aob]], [[4b5r]] – TtSAMR + SAM – ''Thermoanaerobacter tengcongensis''<br />
**[[2gis]], [[4aob]], [[4b5r]] – TtSAMR + SAM – ''Thermoanaerobacter tengcongensis''<br />
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**[[6fz0]] - SAMR + SAM - ''Candidatus pelagibacter''<br />
**[[6fz0]] - SAMR + SAM - ''Candidatus pelagibacter''<br />
**[[6c27]] - SAMR + GTP – ''Enterococcus faecalis''<br />
**[[6c27]] - SAMR + GTP – ''Enterococcus faecalis''<br />
**[[6ues]], [[6wlq]], [[6wlr]] - MtSAMR - ''Mycobacterium tuberculosis''<br />
**[[6uet]] - MtSAMR + SAM<br />
**[[6laz]] - BaSAMR + U1 small nuclear ribonucleoprotein + GTP + SAM analog – ''Bifidobacterium angulatum''<br />
**[[6las]], [[6lax]] - BaSAMR + U1 small nuclear ribonucleoprotein + SAM<br />
**[[6lau]] - BaSAMR + U1 small nuclear ribonucleoprotein + SAH<br />
**[[7eaf]] – CsSAMR + SAM  – ''Caldanaerobacter subterraneus''<br />


*S-adenosylhomocysteine riboswitch
*S-adenosylhomocysteine riboswitch or SAH riboswitch


**[[3npn]], [[3npq]] – SAHR + SAH – ''Ralstonia solanacearum''<br />
**[[3npn]], [[3npq]] – SAHR + SAH – ''Ralstonia solanacearum''<br />
**[[6hag]] - SAMR + SAH – proteobacteria - NMR<br />
**[[6hag]] - SAMR + SAH – proteobacteria - NMR<br />
*SAM/SAH riboswitch
**[[6ymk]] – RoSAM/SAH + adenosine derivative + cytidine derivative – ''Roseobacter''<br />
**[[6ylb]], [[6ymm]] – RoSAM/SAH + SAM<br />
**[[6ymi]] – RoSAM/SAH + AMP<br />
**[[6yl5]], [[6yml]] – RoSAM/SAH + SAH<br />
**[[6ymj]] – RoSAM/SAH + adenosine<br />
*NAD+ riboswitch
**[[6tb7]], [[6tf1]], [[6tf2]], [[6tf3]], [[6tfe]], [[6tfg]], [[7d7y]] – CkNAD + ATP derivative – ''Candidatus koribacter''<br />
**[[6tf0]], [[6tff]], [[6tfh]] – CkNAD + NAD<br />
**[[7d7w]], [[7d7x]], [[7d7z]], [[7d81]], [[7d82]] – AbNAD + NAD - ''Acidobacteriaceae bacterium''<br />
**[[7d7v]] – AbNAD + NAD + U1 small nuclear ribonucleoprotein<br />
*ZTP riboswitch
**[[6od9]] – FuZTP – ''Fusobacterium ulcerans''<br />
**[[6wzr]], [[6wzs]] – FuZTP + pyridine derivative<br />


*Lysine riboswitch
*Lysine riboswitch
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**[[4erj]] – TmKR + aminocaproic acid<br />
**[[4erj]] – TmKR + aminocaproic acid<br />
**[[4erl]] – TmKR + Lys + Gly<br />
**[[4erl]] – TmKR + Lys + Gly<br />
**[[3d0x]] - KR - synthetic<br />
**[[3d0x]] - sKR <br />


*Glutamine riboswitch
*Glutamine riboswitch
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*FMN riboswitch
*FMN riboswitch


**[[3f2q]], [[3f2t]], [[3f2w]], [[3f2x]], [[3f2y]], [[3f30]], [[3f4e]] – FnFMNR + FMN – ''Fusobacterium nucleatum''<br />
**[[6wjr]], [[6wjs]] - FnFMNR – ''Fusobacterium nucleatum''<br />
**[[3f2q]], [[3f2t]], [[3f2w]], [[3f2x]], [[3f2y]], [[3f30]], [[3f4e]] – FnFMNR + FMN '<br />
**[[2yie]] - FnFMNR aptamer domain + FMN<br />
**[[2yie]] - FnFMNR aptamer domain + FMN<br />
**[[3f4g]], [[3f4h]] – FnFMNR + flavin derivative<br />
**[[3f4g]], [[3f4h]] – FnFMNR + flavin derivative<br />
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**[[5c45]], [[5kx9]], [[6bfb]] - FnFMNR + inhibitor<br />
**[[5c45]], [[5kx9]], [[6bfb]] - FnFMNR + inhibitor<br />


*Pre-queosine riboswitch
*Pre-queosine riboswitch or PreQ1 riboswitch


**[[3fu2]], [[3k1v]] – BsPreq1R + queosine<br />
**[[3fu2]], [[3k1v]] – BsPreq1R + queosine<br />
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**[[4jf2]], [[5d5l]] – Preq1R + GTP + deaza-aminomethyl guanine – ''Lactobacillus rhamnosus''<br />
**[[4jf2]], [[5d5l]] – Preq1R + GTP + deaza-aminomethyl guanine – ''Lactobacillus rhamnosus''<br />
**[[4rzd]] – Preq1R + GTP + deaza-aminomethyl guanine – ''Faecalibacterium prausnitzii''<br />
**[[4rzd]] – Preq1R + GTP + deaza-aminomethyl guanine – ''Faecalibacterium prausnitzii''<br />
**[[6vuh]], [[6vui]] – Preq1 – ''Caldanaerobacter subterraneus''<br />
**[[6vuh]], [[6vui]] – CsPreq1 – ''Caldanaerobacter subterraneus''<br />
**[[6e1s]], [[6e1t]], [[6e1u]], [[6e1v]], [[6e1w]], [[7e9e]], [[7e9i]] – CsPreq1 + probe<br />
**[[6xkn]], [[6xko]] – Preq1 + GTP + guanine derivative – ''Faecalibacterium prausnitzii<''br />
**[[7rex]] – Preq1 + guanine derivative – ''Carnobacterium antarcticum''<br />


*C-di-GMP riboswitch
*C-di-GMP riboswitch
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*Glycine riboswitch
*Glycine riboswitch


**[[6wlt]], [[6wlu]] – VcGlyR<br />
**[[3owi]], [[3oww]], [[3owz]] – VcGlyR + glycine<br />
**[[3owi]], [[3oww]], [[3owz]] – VcGlyR + glycine<br />
**[[3ox0]], [[3oxe]], [[3oxj]], [[3oxm]] – VcGlyR + GDP + cytidine cyclic phosphate<br />
**[[3ox0]], [[3oxe]], [[3oxj]], [[3oxm]] – VcGlyR + GDP + cytidine cyclic phosphate<br />
**[[3oxb]], [[3oxd]] – VcGlyR (mutant) + GDP + cytidine cyclic phosphate<br />
**[[3oxb]], [[3oxd]] – VcGlyR (mutant) + GDP + cytidine cyclic phosphate<br />
**[[6wll]], [[6wlm]] – FnGlyR<br />
**[[3p49]] – FnGlyR + U1 small nuclear ribonucleoprotein + glycine<br />
**[[3p49]] – FnGlyR + U1 small nuclear ribonucleoprotein + glycine<br />
*Glutamine riboswitch
**[[6qn3]] – Gln II + Gln – ''Prochlorococcus''<br />


*M-Box riboswitch
*M-Box riboswitch
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*T-Box riboswitch
*T-Box riboswitch


**[[4lck]] – sTBR + tRNA-Gly + ribosomal protein YBXF – synthetic<br />
**[[4lck]] – sTBR + tRNA-Gly + ribosomal protein YBXF <br />
**[[4mgn]] – sTBR + tRNA-Gly <br />
**[[4mgn]] – sTBR + tRNA-Gly <br />
**[[6ufm]] – TBR + tRNA – ''Mycolicibacterium smegmatis''<br />
**[[6ufg]], [[6ufh]] – MtTBR + tRNA <br />
**[[6pom]] – BsTBR + tRNA-Gly – Cryo EM<br />


*Tetrahydrofolate riboswitch
*Tetrahydrofolate riboswitch
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**[[3suh]], [[3sux]] – EsTHFR + THF derivative – ''Eubacterium siraeum''<br />
**[[3suh]], [[3sux]] – EsTHFR + THF derivative – ''Eubacterium siraeum''<br />
**[[3suy]] - EsTHFR + cytidine cyclic phosphate<br />
**[[3suy]] - EsTHFR + cytidine cyclic phosphate<br />
**[[4lvv]], [[4lvx]], [[4lvw]], [[4lvy]], [[4lvz]], [[4lw0]] – THFR + purine derivative – synthetic<br />
**[[4lvv]], [[4lvx]], [[4lvw]], [[4lvy]], [[4lvz]], [[4lw0]] – sTHFR + purine derivative <br />
**[[3sd3]] – THFR (mutant) + pteridine derivative – synthetic<br />
**[[3sd3]] – sTHFR (mutant) + pteridine derivative <br />
**[[6q57]] – THFR + pterin derivative – ''Streptococcus mutans''<br />
**[[7kd1]] – SmTHFR – Streptococcus mutans<br />
**[[6q57]] – SmTHFR + pterin derivative <br />


*Fluoride riboswitch
*Fluoride riboswitch
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**[[4ena]] – TpR + Mg + Cs + GTP + F <br />
**[[4ena]] – TpR + Mg + Cs + GTP + F <br />
**[[4enb]] – TpR + Mg + Ir + K + GTP + F <br />
**[[4enb]] – TpR + Mg + Ir + K + GTP + F <br />
**[[5kh8]] – R - synthetic - NMR<br />
**[[5kh8]] – sR - NMR<br />
 
*Manganese riboswitch
 
**[[6n2v]] – Mn + Mn – ''Xanthomonas oryzae"<br />


*Cobalamine riboswitch
*Cobalamine riboswitch
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**[[4frg]], [[4frn]], [[4gma]], [[4gxy]] – CoR + aptamer domain – ''Marine metagenome''<br />
**[[4frg]], [[4frn]], [[4gma]], [[4gxy]] – CoR + aptamer domain – ''Marine metagenome''<br />
**[[6vmy]] – BsCoR <br />
**[[6vmy]] – BsCoR <br />
*YdaO riboswitch
**[[6n5k]], [[6n5n]], [[6n5o]], [[6n5p]], [[6n5q]], [[6n5s]], [[6n5t]], [[6wtl]], [[6wtr]] – hYdaO/mRNA <br />


*yybp-ykoy riboswitch
*yybp-ykoy riboswitch

Revision as of 11:33, 3 March 2022

3D structures of riboswitch3D structures of riboswitch

Updated on 03-March-2022

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Michal Harel
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