Riboswitch 3D structures: Difference between revisions

Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}

{{#tree:id=OrganizedByTopic|openlevels=0|

*Adenine riboswitch

**[[1y26]], [[4tzx]], [[4tzy]], [[4xnr]], [[5swd]], [[5swe]], [[5uza]], [[6vwt]], [[6vwv]] – VvAR + adenine – ''Vibrio vulnificus''<br />

**[[5e54]] – VvAR <br />

**[[3ivn]] – BsAR (mutant) – ''Bacillus subtilis''<br />

**[[3la5]] - BsAR (mutant) + azacytosine<br />

*Guanine riboswitch

**[[1y27]] – BsGR residues 185-252 + guanine<br />  

**[[2g9c]], [[3fo4]], [[3fo6]], [[3ges]], [[3gog]], [[3rkf]] - BsGR (mutant) + guanine derivative<br />

**[[6p2h]] – sGR <br />

**[[2b57]] – GR + purine derivative<br />

*Guanidine riboswitch

**[[5nwq]], [[5ny8]], [[5nz3]], [[5nz6]], [[5o62]] – TfGNR + guanidine derivative – ''Thermobifida fusca''<br />

**[[5o69]] – TfGNR + agmatine <br />

**[[5ndh]], [[5ndi]], [[5nef]], [[5neo]], [[5nep]], [[5neq]], [[5nex]], [[5nom]] – GNR + guanidine derivative – ''Gloeobacter violaceus'' <br />

**[[5vj9]], [[5vjb]] – GNR + guanidine – ''Pseudomonas aeruginosa'' <br />

*Xanthine riboswitch

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

*Thiamine pyrophosphate riboswitch

**[[2gdi]] – TPPR + TPP – synthetic

**[[2hoj]], [[2hok]], [[2hol]] – EcTPPR + TPP + metal ion – ''Escherichia coli''

**[[4nyg]], [[7td7]], [[7tda]], [[7tdb]] – EcTPPR + thiamine derivative<br />

**[[2cky]], [[3d2g]], [[3d2v]], [[3d2x]] - TPPR + TPP analog – ''Arabidopsis thaliana''

*S-adenosylmethionine riboswitch or SAM riboswitch

**[[2gis]], [[4aob]], [[4b5r]], [[4l81]] – TtSAMR + SAM – ''Thermoanaerobacter tengcongensis''

**[[3iqr]], [[2ydh]], [[2ygh]] - TtSAMR (mutant) + SAM

S-adenosylhomocysteine riboswitch or SAH riboswitch

**[[3npn]], [[3npq]] – SAHR + SAH – ''Ralstonia solanacearum''

**[[6hag]] - SAMR + SAH – ''proteobacteria'' - NMR<br />

*SAM/SAH riboswitch

**[[6ymk]] – RoSAM/SAH + adenosine derivative + cytidine derivative – ''Roseobacter''<br />

**[[6ylb]], [[6ymm]] – RoSAM/SAH + SAM<br />

**[[7d7w]], [[7d7x]], [[7d7z]], [[7d81]], [[7d82]] – AbNADR + NAD - ''Acidobacteriaceae bacterium''<br />

**[[7d7v]] – AbNADR + NAD + U1 small nuclear ribonucleoprotein<br />

*Lysine riboswitch

**[[3d0u]] – TmKR ligand-binding domain + Lysine – ''Thermotoga maritime''

**[[4erj]] – TmKR + aminocaproic acid<br />

**[[4erl]] – TmKR + Lys + Gly<br />

*FMN riboswitch

**[[6wjr]], [[6wjs]] - FnFMNR – ''Fusobacterium nucleatum''<br />

**[[3f2q]], [[3f2t]], [[3f2w]], [[3f2x]], [[3f2y]], [[3f30]], [[3f4e]] – FnFMNR + FMN

**[[2yif]] - FnFMNR + GTP

**[[6bfb]] – FnFMNR + inhibitor<br />

*Pre-queosine riboswitch

**[[3fu2]], [[3k1v]] – BsPreq1R + queosine

**[[3gca]] – TtPreq1R + queosine

**[[4qk8]], [[4qka]] – GMPR + GTP – ''Thermoanaerobacter pseudethanolicus''<br />

**[[4qk9]] – GMPR + guanosine derivative – ''Thermovirga lienii''<br />

*Glycine riboswitch

**[[6wlt]], [[6wlu]] – VcGlyR<br />

**[[3owi]], [[3oww]], [[3owz]] – VcGlyR + glycine

**[[6wll]], [[6wlm]] – FnGlyR<br />

**[[3p49]] – FnGlyR + U1 small nuclear ribonucleoprotein + glycine

*Glutamine riboswitch

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

*M-Box riboswitch

**[[3pdr]] – BsMBR + Mn

*T-Box riboswitch

**[[4lck]] – sTBR + tRNA-Gly + ribosomal protein YBXF – synthetic<br />

**[[4mgn]] – sTBR + tRNA-Gly <br />

**[[6ufg]], [[6ufh]] – MtTBR + tRNA <br />

**[[6pom]] – BsTBR + tRNA-Gly – Cryo EM<br />

*Tetrahydrofolate riboswitch

**[[3suh]], [[3sux]] – EsTHFR + THF derivative – Eubacterium siraeum

**[[3suy]] - EsTHFR + cytidine cyclic phosphate

[[4ena]] – TpFR + Mg + Cs + GTP + F <br />

[[4enb]] – TpFR + Mg + Ir + K + GTP + F <br />

*Manganese riboswitch

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

*Cobalamine riboswitch

**[[6vmy]], [[8fw4]] – BsCoR <br />

**[[8sa2]], [[8sa3]], [[8sa4]], [[8sa5]], [[8sa6]] – BsCoR – Cryo EM<br />

*YdaO riboswitch

**[[6n5k]], [[6n5n]], [[6n5o]], [[6n5p]], [[6n5q]], [[6n5s]], [[6n5t]], [[6wtl]], [[6wtr]] – hYdaO/mRNA <br />

* yybp-ykoy riboswitch

**[[4y1i]] – LlYYR + Mn – ''Lactobacillus lactis''<br />

**[[4y1j]] – LlYYR (mutant) + Mn<br />

**[[6cb3]], [[6cc1]], [[6cc3]] – LlYYR + GTP<br />

**[[4y1m]] – EcYYR <br />

* PRPP riboswitch

**[[6dnr]] – SlPRPPR + GTP + cytidine phosphate – ''Syntrophothermus lipocalidus''<br />

**[[6dlq]], [[6dls]], [[6dlt]] – SlPRPPR + GTP + cytidine phosphate + PRP<br />

**[[6ck5]] – TmPRPPR + PRPP – ''Thermoanaerobacter mathranii''<br />

**[[6ck4]] – TmPRPPR (mutant) + G4P<br />

* PPGPP riboswitch

**[[6dme]], [[6dmd]], [[6dmc]] – SaPPGPPR + GTP + cytidine phosphate + guanine tetraphosphate – ''Sulfobacillus acidophilus''<br />

*PFI riboswitch

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

*NiCo riboswitch

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

*ZMP riboswitch

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

*ZTP riboswitch

**[[6od9]] – FuZTP – ''Fusobacterium ulcerans''<br />

**[[6wzr]], [[6wzs]] – FuZTP + pyridine derivative<br />

**[[5btp]] – FuZTPR + AICAR <br />

*Deoxyguanosine riboswitch

**[[3sk4]], [[3ski]], [[3skl]], [[3skt]], [[3skz]], [[3slm]], [[3slq]] – DgR + guanosine derivative<br />

*ThiM riboswitch

**[[7tzr]], [[7tzs]], [[7tzt]], [[7tzu]] – EcThR + quinoxaline derivative <br />

**[[3k0j]] – EcThR + thiamine pyrophosphate