Riboswitch 3D structures: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
Michal Harel (talk | contribs)
31,761 edits
No edit summary
Michal Harel (talk | contribs)
31,761 edits
No edit summary
 
(One intermediate revision by the same user not shown)
Line 92: Line 92:
**[[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 />
*ZTP riboswitch
**[[6od9]] – FuZTP – Fusobacterium ulcerans<br />
**[[6wzr]], [[6wzs]] – FuZTP + pyridine derivative<br />


*Lysine riboswitch
*Lysine riboswitch
Line 222: Line 217:
**[[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
Line 232: Line 227:
*ZTP riboswitch
*ZTP riboswitch


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


*Deoxyguanosine riboswitch
*Deoxyguanosine riboswitch

Latest revision as of 11:09, 11 August 2024

3D structures of riboswitch3D structures of riboswitch

Updated on 11-August-2024

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

Michal Harel
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=Riboswitch_3D_structures&oldid=4225724"