Riboswitch 3D structures

3D structures of riboswitch3D structures of riboswitch

Updated on 11-August-2024

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• Adenine riboswitch
  • 1y26, 4tzx, 4tzy, 4xnr, 5swd, 5swe, 5uza, 6vwt, 6vwv – VvAR + adenine – Vibrio vulnificus
    
  • 5e54 – VvAR
    
  • 3ivn – BsAR (mutant) – Bacillus subtilis
    
  • 3la5 - BsAR (mutant) + azacytosine
    
• Guanine riboswitch
  • 1y27 – BsGR residues 185-252 + guanine
    
  • 2g9c, 3fo4, 3fo6, 3ges, 3gog, 3rkf - BsGR (mutant) + guanine derivative
    
  • 3got - BsGR (mutant) + adenine derivative
    
  • 2xo1 - BsGR aptamer domain + adenine derivative
    
  • 3g4m, 3ger - BsGR + guanine derivative
    
  • 2xnz, 6ubu, 6uc7, 6uc8, 6uc9 - BsGR aptamer domain + guanine derivative
    
  • 2xo0 - BsGR aptamer domain + triazine derivative
    
  • 5c7u, 5c7w - BsGR + hypoxanthine
    
  • 2ees, 2eet, 2eeu, 2eev, 2eew - BsGR (mutant) + hypoxanthine
    
  • 3gao - BsGR + xanthine
    
  • 2xnw – BsGR + Mn
    
  • 4fe5, 4fej, 4fel, 4fen, 4feo, 4fep – sGR + hypoxanthine – synthetic
    
  • 6p2h – sGR
    
  • 2b57 – GR + purine derivative
    
• Guanidine riboswitch
  • 5nwq, 5ny8, 5nz3, 5nz6, 5o62 – TfGNR + guanidine derivative – Thermobifida fusca
    
  • 5o69 – TfGNR + agmatine
    
  • 5nzd – TfGNR + CDP derivative
    
  • 7mlw – GNR + guanidine – Burkholderia
    
  • 6hbt, 6hbx, 6hc5 – GNR + guanidine II + inhibitor – Gloeobacter violaceus
    
  • 5t83 – GNR + guanidine – Sulfobacillus acidophilus
    
  • 5ndh, 5ndi, 5nef, 5neo, 5nep, 5neq, 5nex, 5nom – GNR + guanidine derivative – Gloeobacter violaceus
    
  • 5vj9, 5vjb – GNR + guanidine – Pseudomonas aeruginosa
    
• Xanthine riboswitch
  • 7elp, 7elq, 7elr, 7els – XR + xanthine derivative – Ideonella
    
• Thiamine pyrophosphate riboswitch
  • 2gdi – TPPR + TPP – synthetic
  • 2hoj, 2hok, 2hol – EcTPPR + TPP + metal ion – Escherichia coli
  • 2hom, 8f4o– EcTPPR + TMP
  • 2hoo, 2hop – EcTPPR + TPP analog
  • 4nya, 4nyb, 4nyc, 7tdc – EcTPPR + pyrimidine derivative
    
  • 4nyd – EcTPPR + hypoxanthine
    
  • 4nyg, 7td7, 7tda, 7tdb – EcTPPR + thiamine derivative
    
  • 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
  • 3iqp - TtSAMR
  • 2qwy, 3e5c, 3e5e, 3e5f, 3iqn - SAMR + SAM – synthetic
  • 4kqy – BsSAMR + SAM
    
  • 3v7e – BsSAMR + Ybxf + SAM
    
  • 4oqu - SAMR + SAM - synthetic
    
  • 6c27 - SAMR + GTP – Enterococcus faecalis
    
  • 6ues, 6wlq, 6wlr - MtSAMR – Mycobacterium tuberculosis
    
  • 6uet - MtSAMR + SAM
    
  • 3gx5, 3gx6, 3gx7 - TtSAMR + SAM
    
  • 6laz - BaSAMR + U1 small nuclear ribonucleoprotein + GTP + SAM analog – Bifidobacterium angulatum
    
  • 6las, 6lax - BaSAMR + U1 small nuclear ribonucleoprotein + SAM
    
  • 6lau - BaSAMR + U1 small nuclear ribonucleoprotein + SAH
    
  • 7eaf – CsSAMR + SAM – Caldanaerobacter subterraneus
    

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
  • 6tb7, 6tf1, 6tf2, 6tf3, 6tfe, 6tfg, 7d7y – CkNADR + ATP derivative – Candidatus koribacter
    
  • 6tf0, 6tff, 6tfh – CkNADR + NAD
    
  • 8gxc, 8hb1, 8hb8, 8i3z – SmNADR II + NMN
    
  • 8gxb, 8hba – SmNADR II + NAD
    
  • 8hb3 – SmNADR II + NR
    
  • 7d7w, 7d7x, 7d7z, 7d81, 7d82 – AbNADR + NAD - Acidobacteriaceae bacterium
    
  • 7d7v – AbNADR + NAD + U1 small nuclear ribonucleoprotein
    
• Lysine riboswitch
  • 3d0u – TmKR ligand-binding domain + Lysine – Thermotoga maritime
  • 4erj – TmKR + aminocaproic acid
    
  • 4erl – TmKR + Lys + Gly
    
• FMN riboswitch
  • 6wjr, 6wjs - FnFMNR – Fusobacterium nucleatum
    
  • 3f2q, 3f2t, 3f2w, 3f2x, 3f2y, 3f30, 3f4e – FnFMNR + FMN
  • 2yie - FnFMNR aptamer domain + FMN
  • 3f4g, 3f4h – FnFMNR + flavin derivative
  • 2yif - FnFMNR + GTP
  • 6bfb – FnFMNR + inhibitor
    
• 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
  • 6wlt, 6wlu – VcGlyR
    
  • 3owi, 3oww, 3owz – VcGlyR + glycine
  • 3ox0, 3oxe, 3oxj, 3oxm – VcGlyR + GDP + cytidine cyclic phosphate
  • 3oxb, 3oxd – VcGlyR (mutant) + GDP + cytidine cyclic phosphate
  • 6wll, 6wlm – FnGlyR
    
  • 3p49 – FnGlyR + U1 small nuclear ribonucleoprotein + glycine
• Glutamine riboswitch
  • 6qn3 – GlnR II + Gln – Prochlorococcus
    
• M-Box riboswitch
  • 3pdr – BsMBR + Mn
• 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

• • 6vmy, 8fw4 – BsCoR
    
  • 8sa2, 8sa3, 8sa4, 8sa5, 8sa6 – BsCoR – Cryo EM
    
• YdaO riboswitch
  • 6n5k, 6n5n, 6n5o, 6n5p, 6n5q, 6n5s, 6n5t, 6wtl, 6wtr – hYdaO/mRNA
    
• 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
  • 3sk4, 3ski, 3skl, 3skt, 3skz, 3slm, 3slq – DgR + guanosine derivative
    
• ThiM riboswitch
  • 7tzr, 7tzs, 7tzt, 7tzu – EcThR + quinoxaline derivative
    
  • 3k0j – EcThR + thiamine pyrophosphate