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Sigma factor 3D structures

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Revision as of 09:52, 20 November 2023 by Michal Harel (Talk | contribs)
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3D structures of sigma factor

Updated on 20-November-2023 {{#tree:id=OrganizedByTopic|openlevels=0|

  • Sigma factor
    • 1ku2 – TaSF-A region 1.2-3.1 – Thermus aquaticus
    • 1ku3 – TaSF-A region 4 (mutant)
    • 3les – TaSF-A residues 93-271
    • 1sig – EcSF-70 – Escherichia coli
    • 2mao – EcSF-E region 2 - NMR
    • 6fi7 – EcSF-38 - NMR
    • 1tty – TmSF-70 region 4 – Thermotoga maritima
    • 2k6x – TmSF-70 region 1.1 (mutant) - NMR
    • 2ahq – AaSF-54 C terminal – Aquifex aeolicus - NMR
    • 2k9l, 2k9m – AaSF-54 core domain - NMR
    • 3mzy – SFH – Fusobacterium nucleatum
    • 1h3l – ScSF N terminal – Streptomyces coelicolor
    • 5fgm – ScSF-R region 4
    • 7qh5 – SF-G1 – Streptomyces tsukubensis
    • 5mww – BsSF-A region 1.1 - Bacillus subtilis - NMR
    • 8b3z – BsSF-E N terminal
    • 5xe7 – MtSF-J – Mycobacterium tuberculosis
  • Sigma factor complex with DNA
    • 3ugo, 3ugp - TaSF-A region 2 + DNA
    • 1ku7 – TaSF-A region 4 (mutant) + DNA
    • 4ki2 - TaSF-A region 2-3 + DNA
    • 2h27 – EcSF-E region 4 + DNA
    • 2map – EcSF-E region 2 + DNA - NMR
    • 2o8k, 2o9l – AaSF-54 C terminal + DNA - NMR
    • 5ui5 – AaSF-54 residues 61-398 + DNA
    • 6jhe – BsSF-W region 4 + DNA
  • Sigma factor complex with anti-sigma factor
    • 1tlh – EcSF-70 region 4 + anti-σ factor
    • 1rp3, 1sc5 – AaSF-28 + anti-σ factor FLGM
    • 6ivu – CtSF-1 + anti-σ factor – Clostridium thermocellum
    • 5wur – BsSF-W + anti-σ factor
    • 5uxx – SF + anti-σ factor – Bartonella quintana
    • 4nqw – MtSF-K region 4 + anti-σ factor
  • Sigma factor complex with protein
    • 3lev – TaSF-A residues 93-271 + antibody
    • 1l9u – TaSF-A region 1.1-4 + RNAP subunits α,β,β’,ω
    • 1or7 – EcSF-E + σ-E factor negative regulatory protein
    • 4lup – EcSF-E residues 3-92 + EcSF region 2
    • 2p7v – EcSF-70 region 4 + regulator of σ D
    • 4yg2, 5uag, 5uaj, 5uaq – EcSF-70 + RNAP subunits α,β,β’,ω
    • 5ui8 – EcSF-45 + RNAP subunits α,β,β’,ω
    • 6byu – EcSF-70 + RNAP subunits α,β,β’,ω + ppApp
    • 4mey, 4ljz, 4lk1, 6cux – EcSF-70 + RNAP subunits α,β,β’,ω
    • 6c9y, 6ca0 – EcSF-70 + RNAP subunits α,β,β’,ω - Cryo EM
    • 5byh – EcSF-45 + RNAP subunits α,β,β’,ω
    • 5nwt – EcSF-54 + RNAP subunits α,β,β’,ω
    • 5w1s – EcSF-70 + RNAP subunits α,β,β’ + TraR
    • 5vsw – EcSF-70 + RNAP subunits α,β,β’ + DnaK suppressor protein
    • 5w1t – EcSF-70 + RNAP subunits α,β,β’ + RpoZ + DnaK suppressor protein
    • 4lk0, 4llg, 4yfk, 4yfn, 4yfx, 4zh2 – EcSF-70 + EcRNAP subunits α,β,β’,ω + RNAP inhibitor
    • 3hug – MtSF-L + membrane protein
    • 4x8k – MtSF-A region 2 + RBPA
    • 6onu, 6ono – MtSF-A region 4 + WHIB1
    • 5zx3 – MtSF-H + RNAP subunits α,β,β’,ω
    • 6fbv – MtSF-A + RNAP subunits α,β,β’,ω - Cryo EM
    • 7pp4, 7q4u, 7q59, 7zf2 – MtSF-B + RNAP subunits α,β,β’,ω - Cryo EM
    • 6c05, 6c06 – MtSF-A + RNAP subunits α,β,β’,ω + RbpA - Cryo EM
    • 3wod, 2a6e, 2cw0, 5tmf – TtSF-A + RNAP subunits α,β,β’,ω - Thermus thermophilus
    • 2be5 – TtSF-70 + RNAP subunits α,β,β’,ω + inhibitor
    • 6pfj, 6pfv – ScSF (mutant) + AMFC protein
    • 5tmc – TtSF-A + RNAP subunits α,β,β’,ω + protein + G4P
    • 5xj0 – TtSF-A + RNAP subunits α,β,β’,ω + GP39 + GP76
    • 5x22 – TtSF-A + RNAP subunits α,β,β’,ω + GpA + CMPcPP
    • 4lk0, 4llg, 4yfk, 4yfn, 4yfx, 4zh2 – EcSF7-0 + EcRNAP subunits α,β,β’,ω + RNAP inhibitor
    • 4cxf – SF CNRH + CNRY – Cupriavidus metallidurans
    • 4g6d, 4g8x, 4g94 – SF-70 region 4 + Orf067 – Staphylococcus aureus
    • 5yix – CcSF-70 + GcrA - Caulobacter crescentus
    • 6in7 – PaSF-H + ALGU – Pseudomonas aeruginosa
    • 6eyd – MsSF-A + RNAP subunits α,β,β’,ω - Mycobacterium smegmatis – Cryo EM
    • 6dxo – SvSF-A + BLDN – Streptomyces venezuelae
    • 7vf9 – PaSF-38 + RNAP subunits α,β,β’,ω - Cryo EM
  • E. coli sigma factor-70 complex with protein, DNA and RNA
    • 6p1k, 7khb – EcSF-70 + EcRNAP subunits α,β,β’,ω - Cryo EM
    • 6vjs – EcSF-70 + EcRNAP subunits α,β,β’,ω
    • 3iyd – EcSF-70 in transcription initiation complex + catabolite gene activator
    • 4jk1, 4jk2, 4jkr – EcSF-70 + EcRNAP subunits α,β,β’,ω + G4P
    • 7khe, 7khi – EcSF-70 + EcRNAP subunits α,β,β’,ω + G4P – Cryo EM
    • 7khc – EcSF-70 + EcRNAP subunits α,β,β’,ω + POP – Cryo EM
    • 4yln, 4ylo, 4ylp, 6n62, 6utv, 6utw, 6utx 6uty, 6utz, 6uu0, 6uu1, 6uuc 6uu3, 6uu4, 6uu5, 6uu6, 6uu7, 6uu8, 6uu2, 6uua, 6uuc – EcSF-70 in transcription initiation complex
    • 6b6h, 6xl5, 6xl9, 6xlj, 6xll, 7vwy, 8igr, 8igs – EcSF-70 in transcription activation complex - Cryo EM
    • 5nss – EcSF-54 + EcRNAP subunits α,β,β’,ω + phage shock protein F + DNA - Cryo EM
    • 5nsr, 6gh6, 6gh5, 6gfw, 7szk – EcSF-54 + EcRNAP subunits α,β,β’,ω + DNA - Cryo EM
    • 7bef, 7beg, 7chw, 7mkd, 7mke, 7mki, 7mkj – EcSF-70 + EcRNAP subunits α,β,β’,ω + DNA - Cryo EM
    • 6n61 – EcSF-70 + EcRNAP subunits α,β,β’,ω + capistruin + DNA
    • 6n60 – EcSF-70 + EcRNAP subunits α,β,β’,ω + microcin + DNA
    • 6p18 – EcSF-70 in transcription antitermination complex + protein Q
    • 6jnx, 7ubm – EcSF-70 in transcription antitermination complex + protein Q – Cryo EM
    • 7ubn – EcSF-70 in transcription antitermination complex + NusA – Cryo EM
    • 6jbq – EcSF-E in transcription initiation complex – Cryo EM
    • 5vt0 – EcSF-70 + EcRNAP subunits α,β,β’,ω + RNA – Cryo EM
    • 6k4y – EcSF-70 + EcRNAP subunits α,β,β’,ω + anti-SF + MOTA + DNA – Cryo EM
    • 6ldi, 6xh7, 6xh8, 7c17 – EcSF-70 in transcription activation complex + CueR – Cryo EM
    • 6pb4, 6pb5, 6pb6 – EcSF-70 in transcription activation complex + Crp – Cryo EM
    • 7vwz – EcSF-70 in transcription activation complex + right origin-binding protein – Cryo EM
    • 7w5w, 7w5x, 7w5y – EcSF-70 in transcription activation complex + SoxS – Cryo EM
    • 8jo2 – EcSF-70 in transcription activation complex + BasR – Cryo EM
    • 6n57, 6n58 – EcSF-70 in transcription initiation complex + Tsar – Cryo EM
    • 6psq, 6psr, 6pss, 6pst, 6psu, 6psv, 6psw – EcSF-70 in transcription initiation complex + Trar – Cryo EM
    • 6n4c, 6oul – EcSF-70 in transcription initiation complex – Cryo EM
    • 6wrg – EcSF-70 in transcription initiation complex + GTP – Cryo EM
    • 7chw, 7khb – EcSF-70 in transcription open promoter complex – Cryo EM
    • 6wmu, 7c97, 7dy6 – EcSF-70 in transcription open promoter complex + SspA – Cryo EM
    • 7khi – EcSF-70 in transcription open promoter complex + DKSA + G4P – Cryo EM
    • 7khc – EcSF-70 in transcription closed promoter complex – Cryo EM
    • 6xlm, 7n4e, 7xui – EcSF-70 in elongation complex – Cryo EM
  • Other sigma factor complex with protein, DNA and RNA 
transcription complex
    • 6wox, 6woy – TtSF-A in initial transcription complex + CPT
    • 1smy – TtSF + RNAP subunits α,β,β’,ω + G4P
    • 5voi – TtSF-A + TtRNAP subunits α,β,β’,ω + DNA
    • 7eh2, 7mlb – TtSF-A in transcription initiation complex
    • 5d4c – TtSF-A in transcription initiation complex + CTP + ATP
    • 5d4d – TtSF-A in transcription initiation complex + CTP + NAD
    • 5d4e – TtSF-A in transcription initiation complex + CTP + dephosphate-CoA
    • 5x22, 7eh0, 7eh1 – TtSF-A in transcription initiation complex + CMPPP
    • 5i2d – TtSF-A in transcription activation complex + transcriptional regulator
    • 7f75 – BsSF-A in transcription activation complex + transcriptional regulator – Cryo EM
    • 7ckq – BsSF-A in transcription activation complex + multidrug regulator + YKZG – Cryo EM
    • 3n97 – TaSF-A region 4 + RNAP subunits α + DNA
    • 4xln, 4xlp, 4xlq, 5tjg – TaSF-A in transcription initiation complex
    • 1l9z – TaSF-A + RNAP subunits α,β,β’,ω + DNA – Cryo EM
    • 4xlr, 4xls – TaSF-A in transcription initiation complex + CarD-like transcriptional regulator
    • 1rio - TaSF-A region 4 + repression protein CI + DNA
    • 5uha, 5uh5, 5uh8, 5uh9, {{7u22]] – MtSF-A in transcription initiation complex
    • 6dcf – MtSF-A in transcription initiation complex + RbpA
    • {{8hih]] – MtSF-A in transcription initiation complex + transctriptional regulatory protein – Cryo EM
    • 6c04, 7kin – MtSF-A + RNAP subunits α,β,β’,ω + RbpA + DNA - Cryo EM
    • 7kif, 7kim – MtSF-A + RNAP subunits α,β,β’,ω + WhiB7 + DNA - Cryo EM
    • 5uhe, 5uhf – MtSF-A in transcription initiation complex + inhibitor
    • 6jcy, 6jcx, 5zx2 – MtSF-H in transcription initiation complex
    • 6kon, 6koo, 6kop, 6koq – MtSF-H in transcription initiation complex
    • 6dve, 6dvd, 7rwi – MtSF-L in transcription initiation complex
    • 6dvc, 6dvb, 6dv9, 6tye, 6tyf, 6tyg – MtSF-L in transcription initiation complex
    • 5tw1, 6cce – MsSF-A in transcription initiation complex + peptide - Mycobacterium smegmatis
    • 5vi5, 5vi8, 6vvv – MsSF-A in transcription initiation complex
    • 7p5x – MsSF-A in transcription initiation complex + PafBC – Cryo EM
    • 8i24 – AtSF-I6 + RNAP subunits α,β,β’,ω + DNA – Acetivibrio thermocellum - Cryo EM
    • 8i23 – AtSF-I1 + RNAP subunits α,β,β’,ω + DNA - Cryo EM
    • 7ye1 , 7ye2 – CcSF-70 + RNAP subunits α,β,β’,ω + DNA + GcrA – Cryo EM
    • 7f0r – PaSF-38 in transcription activation complex + SutA – Cryo EM
    • 7xl3, 7xl4 – PaSF-S in transcription activation complex + SutA – Cryo EM
    • 7xya – PaSF-70 in transcription antitermination complex + ALPA – Cryo EM
    • 8gzg, 8gzh – SF-A + RNAP subunits α,β,β’,ω + DNA + RNA – Synechocystis - Cryo EM
    • 8h40 – AnSF-A + RNAP subunits α,β,β’,ω + DNA + NtcA – Anabaena - Cryo EM
    • 8h3v – AnSF-A + RNAP subunits α,β,β’,ω + DNA + NtcA + NtcB - Cryo EM
    • 7vpd, 7vpz, 7x74, 7x75, 7x76 – ScSF-A + RNAP subunits α,β,β’,ω + metal uptake regulation protein + DNA + RNA - Cryo EM
    • 68hkc – EcSF-32 in transcription initiation complex – Cryo EM
    • 6pmi, 6pmj – EcSF-28 in transcription initiation complex – Cryo EM
    • 5ipl, 5ipm, 5ipn – EcSF-38 in transcription initiation complex
    • 8dy7, 8dy9 – SvSF-A + RNAP subunits α,β,β’,ω + WhiA + WhiB + RbpA + DNA - Cryo EM


  • Sigma factor complex with protein and DNA and antibiotics
    • 4oin, 4oip, 4oiq, 4oir, 5x21 – TtSF-A in transcription initiation complex + antibiotic
    • 6cuu – TtSF-A + TtRNAP subunits α,β,β’,ω + DNA + antibiotic
    • 2a68, 2a69, 2a6h, 3dxj, 3eql, 4mq9 – TtSF-70 + RNAP subunits α,β,β’,ω + antibiotic
    • 5uhg – MtSF-A in transcription initiation complex + antibiotic + inhibitor
    • 5uh6, 5uhc, 5uhd, 5uhb – MtSF-A in transcription initiation complex + antibiotic
    • 6bzo – MtSF-A in transcription initiation complex + RbpA + antibiotic - Cryo EM
    • 6vvt, 6vvx, 6vvz – MtSF-A in transcription initiation complex + antibiotic – Cryo EM
    • 6vvy, 6vw0 – MtSF-A in transcription open promoter complex + antibiotic – Cryo EM
    • 6m7j – MtSF-A + RNAP subunits α,β,β’,ω + RBPA + DNA + antibiotic – Cryo EM
    • 6eec, 6ee8, 6edt – MtSF-A + RNAP subunits α,β,β’,ω + RBPA + CARD + DNA + antibiotic – Cryo EM
    • 6ccv – MsSF-A in transcription initiation complex + peptide + RbpA + antibiotic
    • 7l7b – SF-A + RNAP subunits α,β,β’,ω + antibiotic – Clostridia bacterium - Cryo EM
    • 4mex, 4kmu, 4kn4, 4kn7, 4xsx, 4xsy, 4xsz 4zh3, 4zh4, 5uac, 5uah, 5ual – EcSF-70 + RNAP subunits α,β,β’,ω + antibiotic
    • 7szj – EcSF-70 + RNAP subunits α,β,β’,ω + antibiotic – Cryo EM


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