Proteopedia

RNA polymerase 3D structures

Revision as of 13:36, 5 January 2020 by Michal Harel (talk | contribs) (New page: == 3D Structures of RNA polymerase == Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}} {{#tree:id=OrganizedByTopic|openlevels=0| *Prokaryotic DNA-dependent RN...)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)

3D Structures of RNA polymerase3D Structures of RNA polymerase

Updated on 05-January-2020 {{#tree:id=OrganizedByTopic|openlevels=0|

  • Prokaryotic DNA-dependent RNAP
    • 2y0s – SsRNAP – Sulfolobus shibata
    • 1ryq - PfRNAP subunit ε - Pyrococcus furiosus
    • 1go3 – MjRNAP subunit RPB4, RPB7 - Methanocaldococcus jannaschii
    • 1iw7, 1smy, 6asg - TtRNAP subunits α,β,β',ω Thermus thermophilus
    • 1doq - TtRNAP subunit α
    • 3lti– EcRNAP subunit β fragment – Escherichia coli
    • 4iqz - EcRNAP subunit β’
    • 3k4g, 1coo - EcRNAP subunit 
    • 1bdf - EcRNAP subunit α mutant)
    • 3lu0 - EcRNAP subunits α,β,β',ω – Electron diffraction
    • 2krc - BsRNAP subunit δ N-terminal – Bacillus subtilis – NMR
    • 2ly7 - BsRNAP subunit β NMR
    • 2m4k - BsRNAP subunit δ NMR
    • 4nc7, 4nc8 - BsRNAP subunit δ
    • 2max - HpRNAP subunit α - Helicobacter pylori - NMR
    • 1qyp – RNAP II C terminal – Thermococcus celer – NMR
    • 4kbj – MtuRNAP β subunit – Mycobacterium tuberculosis
    • 5uh7 - MtuRNAP subunit ’
    • 4noi – RNAP α subunit – Campylobacter jejuni
    • 1hqm – TaRNAP subunits α,β,β',ω Thermus aquaticus
    • 2gho - TaRNAP subunits α,β,β'
    • 2auj, 2auk - TaRNAP subunit β’
    • 1xpp – RNAP subunit L – Thermoplasma acidophilum
    • 2waq, 2wb1, 4ayb – SsRNAP
    • 3e7h – VcRNAP subunit – Vibrio cholera
    • 1ef4 – MtRNAP subunit RPB10 – Methanothermobacter thermautotrophicus
    • 1eik - MtRNAP subunit RPB5 – NMR
    • 4qiw – TkRNAP subunits a’’+d+e’+f+h+k+l+n+p – Thermococcus kodakarensis
    • 4qjf - TkRNAP subunits e’+f
    • 4qjv - TkRNAP subunits d+l
    • 6fed, 6f6w – MsRNAP subunits α,β,β',ω - Mycobacterium smegmatis – Cryo EM
  • Prokaryotic DNA-dependent RNAP complex with DNA/RNA
    • 4v8s – SsRNAP + DNA
    • 3q22, 3q23]], 3q24, 4ff1, 4ff2, 4ff3, 4ff4 – RNAP + DNA – Enterobacteria phage N4
    • 2o5i, 2o5j, 4gzy, 4gzz, 4xln, 4xlr - TtRNAP subunits α,β,β',ω + DNA +RNA
    • 5x22 - TtRNAP subunits α,β,β',ω + DNA + RNA + CMPCPP
    • 5x21 - TtRNAP subunits α,β,β',ω + DNA + RNA + antibiotic
    • [[4wqs, 4xlp, 4xlq, 4xls, 5tjg - TtRNAP subunits α,β,β',ω + DNA
    • 2ppb - TtRNAP subunits α,β,β',ω + antibiotic + DNA + RNA + substrate analog
    • 4yg2, 4jk1, 4jk2, 4jkr, 4kmu - EcRNAP subunits α,β,β',ω RNA
    • 6flp, 6bjs, 6asx, 6alh, 6alf, 6rip, 6ri9 - EcRNAP subunits α,β,β',ω RNA + DNA – Cryo EM
    • 6rh3 - EcRNAP subunits α,β,β',ω RNA + DNA + GMP + CTP – Cryo EM
    • 4kn4, 4kn7 - EcRNAP subunits α,β,β',ω RNA + antibiotic
  • Prokaryotic DNA-dependent RNAP complex with protein
    • 3p8b – PfRNAP subunit ε’’ + transcription antitermination protein
    • 3qqc - PfRNAP subunits β, ε’’ + transcription antitermination protein
    • 2be5- TtRNAP subunits α,β,β’,ω + σ factor + inhibitor
    • 2cw0, 5tmf - TtRNAP subunits α,β,β’,ω + σ factor
    • 3wod - TtRNAP subunits α,β,β’,ω + σ factor + GP39
    • 4mq9 - TtRNAP subunits α,β,β’,ω + σ factor + GE23077
    • 5tmc - TtRNAP subunits α,β,β’,ω + σ factor + protein
    • 3dxj, 3eql - TtRNAP subunits α,β,β’,ω + σ factor + antibiotic
    • 5xj0 - TtRNAP subunits α,β,β’,ω + σ factor + GP39 + GP76
    • 4wqt - TtRNAP subunits α,β,β’,ω + RNA cleavage stimulating factor
    • 3mlq - TtRNAP subunit β + transcription-repair coupling factor
    • 3woe, 3wof - TtRNAP subunit β + GP39
    • 2lmc - EcRNAP subunit β + RNAP inhibitor
    • 3mmp - EcRNAP subunit β + EF-TU
    • 4ljz, 4lk1, 4mey, 4xsx, 4xsy, 4xsz, 4zh2, 4zh3 , 4zh4, 5byh, 5nwt, 5uag, 5uah, 5uaj, 5ual, 5uaq, 5ui8 - EcRNAP subunits α,β,β’,ω + σ factor
    • 6c9y - EcRNAP subunits α,β,β’,ω + σ factor – Cryo EM
    • 4mex - EcRNAP subunits α,β,β’,ω + σ factor + salinamide
    • 4lk0, 4llg, 4mex, 4yfk, 4yfn, 4yfx - EcRNAP subunits α,β,β’,ω + σ factor + RNAP inhibitor
    • 5uac, 6cux - EcRNAP subunits α,β,β’,ω + σ factor + antibiotic
    • 6byu - EcRNAP subunits α,β,β’,ω + σ factor + PPAPP
    • 5w1s - EcRNAP subunits α,β,β’,ω + σ factor + TRAR
    • 6rin, 6ri7 - EcRNAP subunits α,β,β’,ω + GREB + RNA + DNA – Cryo EM
    • 5tbz - EcRNAP subunits α,β,β’ + NusG – Cryo EM
    • 6fbv - MtuRNAP subunits α,β,β’,ω + σ factor – single particle EM
    • 5zx3 - MtuRNAP subunits α,β,β’,ω + σ factor
    • 6dve, 6dvd, 6dvc, 6dvb, 6dv9 - MtuRNAP subunits α,β,β’,ω + σ factor + DNA
    • 5zx2 - MtuRNAP subunits α,β,β’,ω + σ factor + DNA + RNA
    • 3ihq, 1z3e, 3gfk - BsRNAP subunit α + regulatory protein SPX
    • 1l9u - TaRNAP subunits α,β,β’,ω + σ factor
    • 2jzb – RNAP subunit α + NusA transcription elongation factor – Yersinia pseudotuberculosis
    • 3tbi - RNAP subunit β + GP33 – Enterobacteria phage T4
    • 3lpe - MjRNAP subunit ε’’ + transcription antitermination protein
    • 6eyd - MsRNAP subunits α,β,β’,ω + σ factor – Cryo EM
  • Prokaryotic DNA-dependent RNAP complex with σ factor + DNA/RNA
    • 4oin, 4oio - TtRNAP subunits α,β,β’,ω + σ factor + GE23077 + DNA
    • 4oip - TtRNAP subunits α,β,β’,ω + σ factor + GE23077 + DNA + nucleotide
    • 4oiq, 4oir - TtRNAP subunits α,β,β’,ω + σ factor + GE23077 + DNA + antibiotic
    • 4g7h, 4g7o, 4g7z, 4q4z, 5d4d, 5d4e, 5voi, 6p70 - TtRNAP subunits α,β,β’,ω + σ factor + DNA
    • 4q5s, 5d4c, 5e17, 5e18, 5vo8, 6p71, 6oy7, 6oy6, 6oy5, 6ow3, 6ovy, 6ovr - TtRNAP subunits α,β,β’,ω + σ factor + DNA + RNA
    • 5i2d - TtRNAP subunits α,β,β’,ω + σ factor + transcriptional regulator + DNA + RNA
    • 6cuu - TtRNAP subunits α,β,β’,ω + σ factor + DNA + antibiotic
    • 6n62 - EcRNAP subunits α,β,β’,ω + σ factor + DNA
    • 6n61 - EcRNAP subunits α,β,β’,ω + σ factor + DNA + capistruin peptide
    • 6n60 - EcRNAP subunits α,β,β’,ω + σ factor + DNA + microcin peptide
    • 5nsr, 5nss, 6gh6, 6gh5, 6ca0, 6omf - EcRNAP subunits α,β,β’,ω + σ factor + DNA – Cryo EM
    • 5vt0 - EcRNAP subunits α,β,β’,ω + σ factor + RNA – Cryo EM
    • 4yln, 4ylo, 4ylp, 5ipl, 5ipm, 5ipn, 6gfw - EcRNAP subunits α,β,β’,ω + σ factor + DNA + RNA
    • 6b6h - EcRNAP subunits α,β,β’,ω + σ factor + CAP + DNA + RNA – Cryo EM
    • 6k4y - EcRNAP subunits α,β,β’,ω + σ factor + anti-s factor + MOTA + DNA – Cryo EM
    • 3iyd - EcRNAP subunits α,β,β’,ω + σ factor + catabolite gene activator + DNA
    • 4s20 - EcRNAP subunits α,β,β’,ω + σ factor + RAPA + DNA
    • 5ms0 - EcRNAP subunits α,β,β’,ω + σ factor + NusB + NusG + NusA + antitermination protein + RS10 + DNA – Cryo EM
    • 5uha - MtuRNAP subunits α,β,β’,ω + σ factor + DNA
    • 5uh9, 5uh8, 6jcy, 6jcx, 6jbq - MtuRNAP subunits α,β,β’,ω + σ factor + DNA + RNA
    • 5uhg, 5uhc, 5uh6, 5uh5 - MtuRNAP subunits α,β,β’,ω + σ factor + DNA + RNA + antibiotic
    • 5uhd, 5uhb - MtuRNAP subunits α,β,β’,ω + σ factor + DNA + antibiotic
    • 5uhf, 5uhe - MtuRNAP subunits α,β,β’,ω + σ factor + DNA + RNA + inhibitor
    • 1l9z - TaRNAP subunits α,β,β’,ω + σ factor + DNA
  • Prokaryotic DNA-dependent RNAP complex with protein + DNA/RNA
    • 3aoh, 3aoi - TtRNAP subunits α,β,β’,ω + DNA + RNA + GFH1
    • 3t72 - EcRNAP subunit β + Pho box DNA + PhoB
    • 1lb2, 3n4m - EcRNAP subunit α + DNA + CAP
    • 1xs9 - EcRNAP subunit α + DNA + MARA
    • 5ciz - EcRNAP subunit α + DNA + CRP
    • 3n97 - EcRNAP subunit α C terminal + DNA + σ factor
    • 6c6u - EcRNAP subunits α,β,β’,ω + NusG + DNA – Cryo EM
    • 6c6t, 6c6s - EcRNAP subunits α,β,β’,ω + RFAH + DNA – Cryo EM
    • 6gov - EcRNAP subunits α,β,β’,ω + NusB + antitermination protein + RS10 + DNA – Cryo EM
    • 6flq - EcRNAP subunits α,β,β’,ω + NusA + DNA + RNA – Cryo EM
    • 6alg - EcRNAP subunits α,β,β’,ω + NUN + DNA + RNA – Cryo EM
    • 6p19 - EcRNAP subunits α,β,β’,ω + protein Q + DNA + RNA – Cryo EM
    • 6jnx - EcRNAP subunits α,β,β’,ω + protein Q + σ factor + DNA – Cryo EM
    • 6p18 - EcRNAP subunits α,β,β’,ω + protein Q + σ factor + DNA + RNA – Cryo EM
    • 6j9f - XoRNAP subunits α,β,β’,ω + P7 + DNA + RNA – Xanthomonas oryzae - Cryo EM
    • 6j9e - XoRNAP subunits α,β,β’,ω + P7 + DNA + RNA + NusA - Cryo EM
  • Prokaryotic DNA-dependent RNAP complex with small molecule
  • Viral DNA-dependent RNAP
    • 6ric – VvRNAP – vaccinia virus – Cryo EM
    • 6rid – VvRNAP + RNA + DNA – Cryo EM
    • 6rie – VvRNAP + mRNA capping enzyme + RNA + DNA – Cryo EM
  • Eukaryotic DNA-dependent RNAP I
  • Eukaryotic DNA-dependent RNAP II
  • Eukaryotic DNA-dependent RNAP II complex with DNA/RNA
  • Eukaryotic DNA-dependent RNAP II complex with protein
    • 3o2q, 3o2s – hRNAP II subunit α C-terminal + symplekin
    • 3j0k, 5iy6, 5iy7, 5iy8, 5iy9, 5iya, 5iyb, 5iyc, 5iyd – hRNAP II + TFIIF – Cryo EM
    • 2lto - hRNAP II subunit RPB1 + Tudor domain containing protein 3
    • 1pqv, 1y1v, 4bbr, 4bbs - yRNAP II + TFIIS
    • 1y1y - yRNAP II + TFIIS + DNA +RNA
    • 1r5u, 3k7a, 3k1f - yRNAP II + TFIIB
    • 4v1o, 5fyw, 5fz5, 5sva - yRNAP II + DNA + TIIF + TBP + mediator – Cryo EM
    • 2l0i – yRNAP C-terminal + RTT103 – NMR
    • 4bxx, 4bxz, 4by1, 4by7 – yRNAP II + RNA + DNA + transcription factor Bye1
    • 5vvr - yRNAP II + DNA + RNA + Rad26 – Cryo EM
    • 6gml – pRNAP II + RNA + DNA + DSIF + NELF – pig – Cryo EM
    • 6gmh – pRNAP II + RNA + DNA + DSIF + PAF + SPT6 – Cryo EM
    • 6exv – pRNAP II + RNA + DNA + amatoxin – Cryo EM
  • Eukaryotic DNA-dependent RNAP II complex with small molecule
  • Eukaryotic DNA-dependent RNAP III
    • 2xub, 2xv4 - hRNAP III subunits RPC3
    • 5afq - hRNAP III subunits RPC3 + RPC32B
    • 2dk8 – RNAP III RPC34 domain - mouse – NMR
    • 2dk5 – hRNAP III winged helix domain (mutant) – NMR
    • 2yu3 - hRNAP III winged helix domain
    • 2ckz, 5fj9, 5fja, 6eu3, 6eu2 - yRNAP III - Cryo EM
    • 5fj8, 6f41 - yRNAP III + DNA + RNA - Cryo EM
    • 6f44, 6f42, 6f40, 6eu1 - yRNAP III + DNA – Cryo EM
    • 6cnf, 6cnd, 6cnc, 6cnb - yRNAP III + DNA + TFIIIB – Cryo EM
    • 5xon - yRNAP III + DNA + RNA + TFIIB + SPT4 + SPT5 – Cryo EM
    • 5xog - yRNAP III + DNA + RNA + SPT5 + KOW5 + ELF1 – Cryo EM
    • 6eu0 - yRNAP III + DNA + TFIIIB + TATA-box-binding protein – Cryo EM
    • 3ayh - fyRNAP III subunit Rpc8+Rpc9
  • Eukaryotic DNA-dependent RNAP I+II+III
  • Eukaryotic DNA-dependent RNAP μ or DNA-directed DNA/RNA polymerase mu
  • Eukaryotic DNA-dependent RNAP mitochondrial
    • 4boc – hRNAP + DNA
    • 6erq, 6erp – hRNAP + DNA + MTTFA + dimethyladenosine transferase
    • 3spa - hRNAP + polypeptide
  • Eukaryotic DNA primase
    • 4lik, 4mhq, 6rb4 - hDNAP small subunit
    • 3q36 – hDNAP large subunit
    • 5i7m – hDNAP large subunit (mutant)
    • 3l9q – hDNAP large subunit P58C domain
    • 5dqo – hDNAP large subunit P58C domain (mutant)
    • 4rr2 - hDNAP small + large subunit
    • 4bpu - hDNAP small (mutant) + large subunit
    • 4ehs – HpDNAP C terminal
    • 4lim, 4mm2 - yDNAP small subunit
    • 3lgb, 6di6, 6dhw - yDNAP large subunit Fe-S domain
    • 6du0, 6dtz, 6dtv, 6di2 - yDNAP large subunit Fe-S domain (mutant)
  • Eukaryotic DNA primase complex
    • 4lil - hDNAP small subunit + UTP
    • 6r4s - hDNAP small subunit + ATP
    • 6r5e, 6r5d, 6r4u, 6r4t - hDNAP small subunit + nucleoside analog
    • 5f0s, 5f0q – hDNAP large subunit C terminal + RNA
    • 4bpw - hDNAP small (mutant) + large subunit + UTP
    • 4bpx - hDNAP small (mutant) + DNA polymerase α catalytic subunit
    • 5exr - hDNAP small + large subunits + DNA polymerase α catalytic subunit


  • Bacterial DNA primase
    • 1d0q - GsDNAP zinc-binding domain - Geobacillus stearothermophilus
    • 1z8s - GsdnaG dnaB binding domain - NMR
    • 2haj - EcdnaG catalytic domain - NMR
    • 1t3w – EcdnaG C-terminal
    • 1eqn, 1dd9, 1dde – EcdnaG catalytic core
    • 5w33 - MtudnaG RPD 112-432
    • 5z51 - MtudnaG helicase-binding domain 482-637
    • 5vaz – dnaG – Pseudomonas aeruginosa
    • 4im9 – VcdnaG C-terminal
    • 3m1m – DNAP RNA polymerase domain – Sulfolobus islandicus
    • 1zt2, 2pa8, 2pmz, 3hkz, 5ofn - SsDNAP small + large subunit – Sulfolobus solfataricus
    • 2au3 – DNAP zinc-binding and RNAP domains – Aquifex aeolicus
    • 1v33 - PhDNAP small subunit – Pyrocuccus horikoshii
    • 1g71 - PfDNAP small subunit
    • 4e2k – SaDNAP – Staphylococcus aureus
    • 2lzn – SaDNAP C terminal – NMR
    • 5guj – BsdnaG RNAP domain
  • Bacterial DNA primase complex
    • 2r6a, 2r6c - GsdnaG helicase binding domain + helicase
    • 4m4w - GsdnaG helicase binding domain + helicase + DnaI
    • 3b39 – EcdnaG catalytic domain + DNA
    • 5w36, 5w35, 5w34 - MtudnaG + DNA
    • 1v34 - PhDNAP small subunit + UTP
    • 4edg, 4edk, 4edr, 4edt, 4edv, 4ee1 – SaDNAP + nucleotide
    • 5of3 - SsDNAP small + large subunit + protein
  • RNA polymerase from Bacteriophage T7 or DNA primase/helicase or GP4
  • RNA-dependent RNAP
  • RNA-dependent RNAP complex with RNA
  • RNA-dependent RNAP complex with protein
    • 3phw, 2pt2, 3pt2 – HfRNAP + ubiquitin
    • 3phx, 3pse – HfRNAP + ISG15
    • 6u5o – HmpvRNAP L + phosphoprotein – Cryo EM
    • 6pzk – RNAP L + phosphoprotein – Human respiratory syncytial virus - Cryo EM
    • 6po2, 6pns – RNAP + VP3 – Bluetongue virus - Cryo EM
    • 2d7s, 2f8e – FmRNAP + VPG
    • 5y3d – MnvRNAP + VPG
    • 3cdw - CvRNAP + POP + VPG
    • 4f5x – SrRNAP + Vp2 + Vp6
    • 3zed – IpnvRNAP + capsid protein Vp3
    • 4hxd – RNAP L + polyubiquitin-C – Dugbe virus
    • 4r71 – RNAP b chain + EF-TS EF-TU + RPS1 – Enterobacteria phage qbeta
    • 5jze – RNAP + ISG15 – Erve virus
    • 6tz0, 6ty8 – BmcpvRNAP + Vp4 – Bombyx mori cytoplasmic polyhedrosis virus – Cryo EM
    • 6tz2, 6tz1, 6ty9, 5h0r – BmcpvRNAP + Vp4 – RNA – Cryo EM
    • 6ogy – RvARNAP + Vp2 + RNA – Cryo EM
    • 6k32 – RvARNAP + Vp1 + Vp4 + RNA – Cypovirus 1 - Cryo EM
  • RNA-dependent RNAP complex with small molecule
  • Influenza virus polymerase acidic protein (or PA or subunit P2) N terminal 1-198


  • Influenza virus polymerase basic protein 2 (or RNAP subunit P3 or PB2)); Domains: cap-binding 318-483; Cap-binding and midlink 247-536; 627 538-693; NLS 694-753
    • 4enf, 4u6o, 4j2r, 2vqz, 5ef9, 5eg9 – IvRNAP PB2 cap-binding domain
    • 3wi0 – IvRNAP PB2 cap-binding domain (mutant)
    • 3cw4 - IvRNAP PB2 627 + NLS domains
    • 2gmo - IvRNAP PB2 627 + NLS domains - NMR
    • 4eqk, 5efa, 5efc – IvRNAP PB2 cap-binding domain + GTP
    • 4nce, 3wi1 – IvRNAP PB2 cap-binding domain (mutant) + GTP derivative
    • 4ncm – IvRNAP PB2 cap-binding domain (mutant) + inhibitor
    • 4p1u, 4yd0, 5buh, 5jun, 5jur - IvRNAP PB2 cap-binding domain + inhibitor
    • 6euy, 6eux, 6euv - IvRNAP PB2 cap-binding + midlink domains + inhibitor
    • 5wl0 - IvRNAP PB2 cap-binding + midlink + 627 + NLS domains + inhibitor
    • 4uad, 4uae, 4uaf - IvRNAP PB2 + importin
    • 2vy6 - IvRNAP PB2 627 + NLS domains
    • 2vy7 - IvRNAP PB2 627 domain
    • 2vy8 - IvRNAP PB2 627 domain (mutant)
  • Influenza virus RNAP PA+PB1
    • 2znl - IvRNAP PA + PB1
    • 3cm8 - IvRNAP PA residues 256-716 + PB1 peptide
  • Influenza virus RNAP PA+PB2
    • 5fml - IvRNAP PA N terminal + PB2 NLS peptide
  • Influenza virus RNAP PB1+PB2
    • 2ztt, 3a1g - IvRNAP PB1 C terminal + RNAP PB2 N terminal
    • 3j9b - IvRNAP PB1+PB2 N terminal + RNA
  • Influenza virus RNAP PA+PB1+PB2 (subunits P1+p2+p3)
  • Poly(A) RNA polymerase
    • 3pq1 – hRNAP (mutant)
    • 4lt6 – hRNAP γ
    • 4nkt – SpRNAP (mutant) + UMPNPP
    • 4nku – SpRNAP (mutant) + RNA
    • 3nyb – yRNAP + AIR2
    • 4e7x, 4e80, 4e8f, 4ep7, 4fh3 – fyRNAP Cid1
    • 4fh5, 4fhp, 4fhv, 4fhw, 4fhy – fyRNAP Cid1 + nucleotide
    • 4ud4, 4ud5 - fyRNAP Cid1 (mutant)
    • 4fhx – fyRNAP Cid1 (mutant) + ATP
    • 4zrl – CeRNAP gld-2 + germline development defective 3 – Caenorhabidis elegans
    • 5jnb – CeRNAP gld-2 (mutant) + RNP-8

}}

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

Michal Harel, Joel L. Sussman, Jaime Prilusky
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=RNA_polymerase_3D_structures&oldid=3139582"