Riboswitch 3D structures: Difference between revisions

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*Guanidine riboswitch
*Guanidine riboswitch


**[[5nwq]] – TfGR + guanidine – ''Thermobifida fusca''<br />
**[[5nwq]], [[5ny8]], [[5nz3]], [[5nz6]], [[5o62]] – TfGNR + guanidine derivative – ''Thermobifida fusca''<br />
**[[5nzd]] – TfGR + CDP derivative<br />
**[[5o69]] – TfGNR + agmatine <br />
**[[7mlw]] – GR + guanidine – ''Burkholderia''<br />
**[[5nzd]] – TfGNR + CDP derivative<br />
**[[6hbt]], [[6hbx]], [[6hc5]] – GR + guanidine II + inhibitor – ''Gloeobacter violaceus''<br />
**[[7mlw]] – GNR + guanidine – ''Burkholderia''<br />
**[[6hbt]], [[6hbx]], [[6hc5]] – GNR + guanidine II + inhibitor – ''Gloeobacter violaceus''<br />
**[[5t83]] – GNR + guanidine – ''Sulfobacillus acidophilus'' <br />
**[[5ndh]], [[5ndi]], [[5nef]], [[5neo]], [[5nep]], [[5neq]], [[5nex]], [[5nom]] – GNR + guanidine derivative – ''Gloeobacter violaceus'' <br />
**[[5vj9]], [[5vjb]] – GNR + guanidine – ''Pseudomonas aeruginosa'' <br />


*Xanthine riboswitch
*Xanthine riboswitch


**[[7elp]], [[7elq]], [[7elr]], [[7els]] – GR + xanthine derivative – ''Ideonella''<br />
**[[7elp]], [[7elq]], [[7elr]], [[7els]] – XR + xanthine derivative – ''Ideonella''<br />


*Thiamine pyrophosphate riboswitch
*Thiamine pyrophosphate riboswitch


**[[2gdi]] – TPPR + TPP – synthetic<br />
**[[2gdi]] – TPPR + TPP – synthetic
**[[2hoj]], [[2hok]], [[2hol]] – EcTPPR + TPP + metal ion – ''Escherichia coli''<br />
**[[2hoj]], [[2hok]], [[2hol]] – EcTPPR + TPP + metal ion – ''Escherichia coli''
**[[2hom]], [[8f4o]] – EcTPPR + TMP<br />
**[[2hom]], [[8f4o]]– EcTPPR + TMP
**[[2hoo]], [[2hop]] – EcTPPR + TPP analog<br />
**[[2hoo]], [[2hop]] – EcTPPR + TPP analog
**[[4nya]], [[4nyb]], [[4nyc]], [[7tdc]] – EcTPPR + pyrimidine derivative<br />
**[[4nya]], [[4nyb]], [[4nyc]], [[7tdc]] – EcTPPR + pyrimidine derivative<br />
**[[4nyd]] – EcTPPR + hypoxanthine <br />
**[[4nyd]] – EcTPPR + hypoxanthine <br />
**[[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''<br />
**[[2gis]], [[4aob]], [[4b5r]], [[4l81]] – TtSAMR + SAM – ''Thermoanaerobacter tengcongensis''
**[[3iqr]], [[2ydh]], [[2ygh]] - TtSAMR (mutant) + SAM<br />
**[[3iqr]], [[2ydh]], [[2ygh]] - TtSAMR (mutant) + SAM
**[[3iqp]] - TtSAMR<br />
**[[3iqp]] - TtSAMR
**[[5fjc]], [[5fk1]], [[5fk2]], [[5fk3]], [[5fk4]], [[5fk5]], [[5fk6]], [[5fkd]], [[5fke]], [[5fkf]], [[5fkg]], [[5fkh]] - TtSAMR + SAM + GTP<br />
**[[2qwy]], [[3e5c]], [[3e5e]], [[3e5f]], [[3iqn]] - SAMR + SAM – synthetic
**[[2qwy]], [[3e5c]], [[3e5e]], [[3e5f]], [[3iqn]] - SAMR + SAM – synthetic<br />
**[[4kqy]] – BsSAMR + SAM<br />
**[[4kqy]] – BsSAMR + SAM<br />
**[[3v7e]] – BsSAMR + Ybxf + SAM<br />
**[[3v7e]] – BsSAMR + Ybxf + SAM<br />
**[[4oqu]] - sSAMR + SAM <br />
**[[4oqu]] - SAMR + SAM - synthetic<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 />
**[[6ues]], [[6wlq]], [[6wlr]] - MtSAMR – ''Mycobacterium tuberculosis''<br />
**[[6uet]] - MtSAMR + SAM<br />
**[[6uet]] - MtSAMR + SAM<br />
**[[3gx5]], [[3gx6]], [[3gx7]] - SAMR + SAM - tengcongensis<br />
**[[3gx5]], [[3gx6]], [[3gx7]] - SAMR + SAM - ''tengcongensis''<br />
**[[6laz]] - BaSAMR + U1 small nuclear ribonucleoprotein + GTP + SAM analog – ''Bifidobacterium angulatum''<br />
**[[6laz]] - BaSAMR + U1 small nuclear ribonucleoprotein + GTP + SAM analog – ''Bifidobacterium angulatum''<br />
**[[6las]], [[6lax]] - BaSAMR + U1 small nuclear ribonucleoprotein + SAM<br />
**[[6las]], [[6lax]] - BaSAMR + U1 small nuclear ribonucleoprotein + SAM<br />
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**[[7eaf]] – CsSAMR + SAM  – ''Caldanaerobacter subterraneus''<br />
**[[7eaf]] – CsSAMR + SAM  – ''Caldanaerobacter subterraneus''<br />


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


**[[3npn]], [[3npq]] – SAHR + SAH – ''Ralstonia solanacearum''<br />
**[[3npn]], [[3npq]] – SAHR + SAH – ''Ralstonia solanacearum''
**[[6hag]] - SAMR + SAH – proteobacteria - NMR<br />
**[[6hag]] - SAMR + SAH – ''proteobacteria'' - NMR<br />


*SAM/SAH riboswitch
*SAM/SAH riboswitch
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**[[6yl5]], [[6yml]] – RoSAM/SAH + SAH<br />
**[[6yl5]], [[6yml]] – RoSAM/SAH + SAH<br />
**[[6ymj]] – RoSAM/SAH + adenosine<br />
**[[6ymj]] – RoSAM/SAH + adenosine<br />
*NAD+ riboswitch
*NAD+ riboswitch
 
**[[6tb7]], [[6tf1]], [[6tf2]], [[6tf3]], [[6tfe]], [[6tfg]], [[7d7y]] – CkNADR + ATP derivative – ''Candidatus koribacter''<br />
**[[6tb7]], [[6tf1]], [[6tf2]], [[6tf3]], [[6tfe]], [[6tfg]], [[7d7y]] – CkNAD + ATP derivative – ''Candidatus koribacter''<br />
**[[6tf0]], [[6tff]], [[6tfh]] – CkNADR + NAD<br />
**[[6tf0]], [[6tff]], [[6tfh]] – CkNAD + NAD<br />
**[[8gxc]], [[8hb1]], [[8hb8]], [[8i3z]]  – SmNADR II + NMN<br />
**[[8gxc]], [[8hb1]], [[8hb8]], [[8i3z]]  – SmNAD II + NMN<br />
**[[8gxb]], [[8hba]] – SmNADR II + NAD<br />
**[[8gxb]], [[8hba]] – SmNAD II + NAD<br />
**[[8hb3]] – SmNADR II + NR<br />
**[[8hb3]] – SmNAD II + NR<br />
**[[7d7w]], [[7d7x]], [[7d7z]], [[7d81]], [[7d82]] – AbNADR + NAD - ''Acidobacteriaceae bacterium''<br />
**[[7d7w]], [[7d7x]], [[7d7z]], [[7d81]], [[7d82]] – AbNAD + NAD - ''Acidobacteriaceae bacterium''<br />
**[[7d7v]] – AbNADR + NAD + U1 small nuclear ribonucleoprotein<br />
**[[7d7v]] – AbNAD + NAD + U1 small nuclear ribonucleoprotein<br />


*ZTP riboswitch
*ZTP riboswitch


**[[6od9]] – FuZTP – ''Fusobacterium ulcerans''<br />
**[[6od9]] – FuZTP – Fusobacterium ulcerans<br />
**[[5btp]], [[6wzr]], [[6wzs]] – FuZTP + pyridine derivative<br />
**[[6wzr]], [[6wzs]] – FuZTP + pyridine derivative<br />


*Lysine riboswitch
*Lysine riboswitch


**[[3dis]] – TmKR – ''Thermotoga maritima''<br />
**[[3d0u]] – TmKR ligand-binding domain + Lysine – ''Thermotoga maritime''
**[[3d0u]] – TmKR ligand-binding domain + Lysine <br />
**[[3dil]], [[3dim]], [[3dio]], [[3dix]], [[3diy]], [[3diz]], [[3dj2]] – TmKR + Lys <br />
**[[3dj0]], [[3dir]] – TmKR + Lys derivative<br />
**[[3dig]] – TmKR + Cys derivative<br />
**[[3diq]] – TmKR + homoArg <br />
**[[4erj]] – TmKR + aminocaproic acid<br />
**[[4erj]] – TmKR + aminocaproic acid<br />
**[[4erl]] – TmKR + Lys + Gly<br />
**[[4erl]] – TmKR + Lys + Gly<br />
**[[3d0x]] - sKR <br />
*Glutamine riboswitch
**[[5ddp]] – QR + glutamine – human<br />
**[[5ddq]], [[5ddr]] – SeQR + glutamine – ''Synechococcus elongatus''<br />
**[[5ddo]] – SeQR + U1 small nuclear ribonucleoprotein<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 '<br />
**[[3f2q]], [[3f2t]], [[3f2w]], [[3f2x]], [[3f2y]], [[3f30]], [[3f4e]] – FnFMNR + FMN
**[[2yie]] - FnFMNR aptamer domain + FMN<br />
**[[2yie]] - FnFMNR aptamer domain + FMN
**[[3f4g]], [[3f4h]] – FnFMNR + flavin derivative<br />
**[[3f4g]], [[3f4h]] – FnFMNR + flavin derivative
**[[2yif]] - FnFMNR + GTP<br />
**[[2yif]] - FnFMNR + GTP
**[[6dn1]], [[6dn2]], [[6dn3]] - FnFMNR + RNA<br />
**[[6bfb]] – FnFMNR + inhibitor<br />
**[[5c45]], [[5kx9]], [[6bfb]] - FnFMNR + inhibitor<br />


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


**[[3fu2]], [[3k1v]] – BsPreq1R + queosine<br />
**[[3fu2]], [[3k1v]] – BsPreq1R + queosine
**[[3gca]] – TtPreq1R + queosine<br />
**[[3gca]] – TtPreq1R + queosine
**[[3q50]], [[3q51]] – TtPreq1R aptamer domain + queosine<br />
**[[3q50]], [[3q51]] – TtPreq1R aptamer domain + queosine
**[[4jf2]], [[5d5l]] – Preq1R + GTP + deaza-aminomethyl guanine – ''Lactobacillus rhamnosus''<br />
**[[4jf2]] – Preq1R + GTP + deaza-aminomethyl guanine – ''Lactobacillus rhamnosus''<br />
**[[4rzd]] – Preq1R + GTP + deaza-aminomethyl guanine – ''Faecalibacterium prausnitzii''<br />
**[[6vuh]], [[6vui]] – CsPreq1 <br />
**[[6vuh]], [[6vui]] – CsPreq1 – ''Caldanaerobacter subterraneus''<br />
**[[6e1s]], [[6e1t]], [[6e1u]], [[6e1v]], [[6e1w]], [[7e9e]], [[7e9i]] – CsPreq1 + probe<br />
**[[6e1s]], [[6e1t]], [[6e1u]], [[6e1v]], [[6e1w]], [[7e9e]], [[7e9i]] – CsPreq1 + probe<br />
**[[6xkn]], [[6xko]] – Preq1 + GTP + guanine derivative – ''Faecalibacterium prausnitzii<''br />
**[[6xkn]], [[6xko]] – Preq1 + GTP + guanine derivative – ''Faecalibacterium prausnitzii''<br />
**[[7rex]], [[8fb3]] – Preq1 + guanine derivative – ''Carnobacterium antarcticum''<br />
**[[7rex]], [[8fb3]] – Preq1 + guanine derivative – ''Carnobacterium antarcticum''<br />
**[[2miy]] – Preq1 + guanine derivative – ''Streptococcus pneumoniae'' - NMR<br />
**[[2miy]] – Preq1 + guanine derivative – ''Streptococcus pneumoniae'' - NMR<br />
**[[8fza]] – EcPreq1 III <br />
**[[8fza]] – EcPreq1 III <br />
**[[2l1v]] – EcPreq1 I + PreQ1 - NMR <br />
**[[2l1v]] – EcPreq1 I + PreQ1 - NMR <br />
 
C-di-GMP riboswitch
*C-di-GMP riboswitch
 
**[[3ucu]], [[3ucz]] – hGMPR + GpG <br />
**[[3ucu]], [[3ucz]] – hGMPR + GpG <br />
**[[3ud3]], [[3ud4]] – hGMPR + GpA <br />
**[[3ud3]], [[3ud4]] – hGMPR + GpA <br />
**[[3irw]], [[3mxh]] – VcGMPR + C-di-GMP + GTP + U1 small nuclear ribonucleoprotein – ''Vibrio cholerae''<br />
**[[3irw]], [[3mxh]] – VcGMPR + C-di-GMP + GTP + U1 small nuclear ribonucleoprotein – ''Vibrio cholerae''
**[[3iwn]], [[4yb1]] – VcGMPR + C-di-GMP + U1 small nuclear ribonucleoprotein<br />
**[[3iwn]] – VcGMPR + C-di-GMP + U1 small nuclear ribonucleoprotein
**[[3mum]], [[3mur]], [[3mut]] - VcGMPR (mutant) + C-di-GMP + U1 small nuclear ribonucleoprotein<br />
**[[3mum]], [[3mur]], [[3mut]] - VcGMPR (mutant) + C-di-GMP + U1 small nuclear ribonucleoprotein
**[[3muv]] - VcGMPR (mutant) + C-di-AMP + U1 small nuclear ribonucleoprotein<br />
**[[3muv]] - VcGMPR (mutant) + C-di-AMP + U1 small nuclear ribonucleoprotein
**[[3q3z]] - GMPR + C-di-GMP – ''Clostridium acetobutylicum''<br />
**[[3q3z]] - GMPR + C-di-GMP – ''Clostridium acetobutylicum''
**[[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 />
**[[4yaz]], [[4yb0]] – GMPR + C-di-GMP - ''Geobacter''<br />
*C-di-AMP riboswitch
**[[4w90]], [[4w92]] – VBsAMPR + C-di-AMP + U1 small nuclear ribonucleoprotein<br />
**[[3muv]] – AMPR + C-di-AMP + U1 small nuclear ribonucleoprotein - synthetic<br />
**[[4qk8]] – AMPR + C-di-AMP + GTP - ''Thermoanaerobacter pseudethanolicus''<br />
**[[4qk8]], [[4qka]] – AMPR + C-di-AMP + GTP - ''Thermoanaerobacter pseudethanolicus''<br />
**[[4qlm]], [[4qln]] – AMPR + C-di-AMP - ''Thermoanaerobacter tengcongensis''<br />
**[[4qk9]] – AMPR + C-di-AMP + GTP derivative - ''Thermovirga lienii''<br />


*Glycine riboswitch
*Glycine riboswitch


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


*Glutamine riboswitch
*Glutamine riboswitch


**[[6qn3]] – Gln II + Gln – ''Prochlorococcus''<br />
**[[6qn3]] – GlnR II + Gln – ''Prochlorococcus''<br />


*M-Box riboswitch
*M-Box riboswitch


**[[3pdr]] – BsMBR + Mn<br />
**[[3pdr]] – BsMBR + Mn
**[[2qbz]] – BsMBR + Mg<br />


*T-Box riboswitch
*T-Box riboswitch


**[[4lck]] – sTBR + tRNA-Gly + ribosomal protein YBXF <br />
**[[4lck]] – sTBR + tRNA-Gly + ribosomal protein YBXF – synthetic<br />
**[[4mgn]] – sTBR + tRNA-Gly <br />
**[[4mgn]] – sTBR + tRNA-Gly <br />
**[[6ufm]] – TBR + tRNA – ''Mycolicibacterium smegmatis''<br />
**[[6ufm]] – TBR + tRNA – ''Mycolicibacterium smegmatis''<br />
Line 191: Line 164:
*Tetrahydrofolate riboswitch
*Tetrahydrofolate riboswitch


**[[3suh]], [[3sux]] – EsTHFR + THF derivative – ''Eubacterium siraeum''<br />
**[[3suh]], [[3sux]] – EsTHFR + THF derivative – Eubacterium siraeum
**[[3suy]] - EsTHFR + cytidine cyclic phosphate<br />
**[[3suy]] - EsTHFR + cytidine cyclic phosphate
**[[4lvv]], [[4lvx]], [[4lvw]], [[4lvy]], [[4lvz]], [[4lw0]] – sTHFR + purine derivative <br />
**[[4lvv]], [[4lvx]], [[4lvw]], [[4lvy]], [[4lvz]], [[4lw0]] – THFR + purine derivative – synthetic
**[[3sd3]] – sTHFR (mutant) + pteridine derivative <br />
**[[3sd3]] – THFR (mutant) + pteridine derivative – synthetic 
**[[1qa4]], [[1qa5]] – NEF anchor domain – NMR
**[[7kd1]] – SmTHFR – Streptococcus mutans<br />
**[[7kd1]] – SmTHFR – Streptococcus mutans<br />
**[[6q57]] – SmTHFR + pterin derivative <br />
**[[6q57]] – SmTHFR + pterin derivative <br />
Line 201: Line 175:
**[[7wii]] – MlTHFR + NPR<br />
**[[7wii]] – MlTHFR + NPR<br />
**[[7wif]] – MlTHFR + H4B<br />
**[[7wif]] – MlTHFR + H4B<br />
 
Fluoride riboswitch


*Fluoride riboswitch
[[3vrs]] – TpFR + Mn + K + F – ''Thermotoga petrophila''<br />
 
[[4en5]] – TpFR + Mg + Tl + F <br />
**[[3vrs]] – TpR + Mn + K + F – ''Thermotoga petrophila''<br />
[[4enc]] – TpFR + Mg + K + F <br />
**[[4en5]] – TpR + Mg + Tl + F <br />
[[4ena]] – TpFR + Mg + Cs + GTP + F <br />
**[[4enc]] – TpR + Mg + K + F <br />
[[4enb]] – TpFR + Mg + Ir + K + GTP + F <br />
**[[4ena]] – TpR + Mg + Cs + GTP + F <br />
**[[4enb]] – TpR + Mg + Ir + K + GTP + F <br />
**[[5kh8]] – sR - NMR<br />


*Manganese riboswitch
*Manganese riboswitch


**[[6n2v]] – Mn + Mn – ''Xanthomonas oryzae"<br />
**[[6n2v]] – MnR + Mn – ''Xanthomonas oryzae''<br />


*Cobalamine riboswitch
*Cobalamine riboswitch


**[[4frg]], [[4frn]], [[4gma]], [[4gxy]] – CoR + aptamer domain – ''Marine metagenome''<br />
[[4frg]], [[4frn]], [[4gma]], [[4gxy]] – CoR + aptamer domain – Marine metagenome<br />
**[[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 />


Line 225: Line 198:
**[[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 />
Line 232: Line 206:
**[[4y1m]] – EcYYR <br />
**[[4y1m]] – EcYYR <br />


*ykkc riboswitch
* PRPP riboswitch


**[[5u3g]] – TpR + gusanidine – ''Dikeya dadantii''<br />
**[[6dnr]] – SlPRPPR + GTP + cytidine phosphate – ''Syntrophothermus lipocalidus''<br />
 
**[[6dlq]], [[6dls]], [[6dlt]] – SlPRPPR + GTP + cytidine phosphate + PRP<br />
*PRPP riboswitch
**[[6dlr]] – SlPRPPR + cytidine phosphate + PRP<br />
 
**[[6ck5]] – TmPRPPR + PRPP – ''Thermoanaerobacter mathranii''<br />
**[[6ck5]] – TmPRR + PRPP – ''Thermoanaerobacter mathranii''<br />
**[[6ck4]] – TmPRPPR (mutant) + G4P<br />
**[[6ck4]] – TmPRR + PPGPP<br />
**[[6dnr]] – SlPRR + GTP + cytidine phosphate – ''Syntrophothermus lipocalidus''<br />
**[[6dlq]], [[6dls]], [[6dlt]] – SlPRR + GTP + cytidine phosphate + PRPP<br />
**[[6dlr]] – SlPRR + cytidine phosphate + PRPP<br />


* PPGPP riboswitch
* PPGPP riboswitch
Line 250: Line 220:
*PFI riboswitch
*PFI riboswitch


**[[4znp]] – sTpR + AICAR <br />
**[[4znp]] – PFIR + AICAR – synthetic<br />


*NICO riboswitch
*NICO riboswitch


**[[4rum]] – sTpR + Co <br />
**[[4rum]] – NICOR + Co – synthetic<br />


*ZMP riboswitch
*ZMP riboswitch


**[[4xw7]], [[4xwf]] – TpR + AICAR – ''Actinomyces odontolyticus'' <br />
**[[4xw7]], [[4xwf]] – ZMPR + AICAR – ''Actinomyces odontolyticus'' <br />


*Guanidine riboswitch
*ZTP riboswitch


**[[5t83]] – TpR + guanidine – ''Sulfobacillus acidophilus'' <br />
**[[5btp]] – ZTPR + AICAR – ''Fusobacterium ulcerans'' <br />
**[[5ndh]], [[5ndi]], [[5nef]], [[5neo]], [[5nep]], [[5neq]], [[5nex]], [[5nom]] – TpR + guanidine derivative – ''Gloeobacter violaceus'' <br />
**[[5vj9]], [[5vjb]] – TpR + guanidine – ''Pseudomonas aeruginosa'' <br />
**[[5ny8]], [[5nz3]], [[5nz6]], [[5o62]] – TfTpR + guanidine derivative<br />
**[[5o69]] – TfTpR + agmatine <br />


*Deoxyguanosine riboswitch
*Deoxyguanosine riboswitch
Line 275: Line 241:


**[[7tzr]], [[7tzs]], [[7tzt]], [[7tzu]] – EcThR + quinoxaline derivative <br />
**[[7tzr]], [[7tzs]], [[7tzt]], [[7tzu]] – EcThR + quinoxaline derivative <br />
**[[3k0j]] – EcThR + thiamine pyrophosphate <br />
**[[3k0j]] – EcThR + thiamine pyrophosphate  
 
}}
}}


[[Category: Topic Page]]
[[Category: Topic Page]]

Revision as of 11:59, 1 November 2023

3D structures of riboswitch3D structures of riboswitch

Updated on 01-November-2023

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
  • ZTP riboswitch
    • 6od9 – FuZTP – Fusobacterium ulcerans
    • 6wzr, 6wzs – FuZTP + pyridine derivative
  • 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
    • 5btp – ZTPR + AICAR – Fusobacterium ulcerans
  • Deoxyguanosine riboswitch
  • ThiM riboswitch

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Michal Harel
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