RNA polymerase: Difference between revisions

Revision as of 10:04, 21 October 2018

spinqualitylabelsall models

Yeast RNA polymerase II elongation complex C complexed with DNA and RNA and Zn+2 (grey) and Mg+2 (green) ions 3m3y. Subunit B1 (grey), B2 (green), B3 (pink), B9 (wheat), B11 (rust), ABC1 (magenta), ABC2 (cyan), ABC3 (red), ABC4 (aqua), ABC5 (blue) (PDB code 3m3y).

Drag the structure with the mouse to rotate

Export Animated Image Print3D

RNA polymerase (RNAP, DNA primase, dnaG) catalyzes the addition of nucleotides to RNA during transcription.
DNA-dependent RNA polymerase catalyzes the transcription of RNA from a DNA template. The DNA-dependent eukaryote RNAP^[1] are divided to
RNAP I (or Pol I) which transcribes ribosomal RNA^[2];
RNAP II (or Pol II) transcribes DNA and most snRNA and microRNA^[3];
RNAP III (or Pol III) transcribes tRNA and 5S ribosomal RNA^[4].
DNA primase (DNAP) is RNAP which catalyzes the synthesis of the RNA primer which complements an ssDNA template and initiates DNA synthesis^[5].
dnaG is a bacterial primase^[6].
For DNA-dependent RNA polymerase see

RNA-dependent RNA polymerase catalyzes the replication of RNA from a RNA template^[7]. An example is the Influenza virus RNA polymerase which is composed of 3 subunits. Subunit PA is involved in cap-snatching. Subunit PB1 is involved in RNA synthesis. Subunit PB2 is involved in RNA replication and transcription. It is implicated in endonuclease cleavage of RNA primers. View of the nucleic acid (1qln; blue: nontemplate strand; cyan: template strand; red:RNA).
See also RNA-directed RNA polymerase.
For RNA-dependent RNA polymerase from Hepatitis C virus - NS5B - see

Poly(A) RNA polymerase catalyzes the addition of long poly(A) tails to mRNA without a template^[8].

↑ Cramer P, Armache KJ, Baumli S, Benkert S, Brueckner F, Buchen C, Damsma GE, Dengl S, Geiger SR, Jasiak AJ, Jawhari A, Jennebach S, Kamenski T, Kettenberger H, Kuhn CD, Lehmann E, Leike K, Sydow JF, Vannini A. Structure of eukaryotic RNA polymerases. Annu Rev Biophys. 2008;37:337-52. doi: 10.1146/annurev.biophys.37.032807.130008. PMID:18573085 doi:https://dx.doi.org/10.1146/annurev.biophys.37.032807.130008
↑ Comai L. Mechanism of RNA polymerase I transcription. Adv Protein Chem. 2004;67:123-55. PMID:14969726 doi:https://dx.doi.org/10.1016/S0065-3233(04)67005-7
↑ Hahn S. Structure and mechanism of the RNA polymerase II transcription machinery. Nat Struct Mol Biol. 2004 May;11(5):394-403. PMID:15114340 doi:https://dx.doi.org/10.1038/nsmb763
↑ Longo DL, Herbert V. Radioassay for serum and red cell folate. J Lab Clin Med. 1976 Jan;87(1):138-51. PMID:1452
↑ Frick DN, Richardson CC. DNA primases. Annu Rev Biochem. 2001;70:39-80. PMID:11395402 doi:https://dx.doi.org/10.1146/annurev.biochem.70.1.39
↑ Naue N, Beerbaum M, Bogutzki A, Schmieder P, Curth U. The helicase-binding domain of Escherichia coli DnaG primase interacts with the highly conserved C-terminal region of single-stranded DNA-binding protein. Nucleic Acids Res. 2013 Apr;41(8):4507-17. doi: 10.1093/nar/gkt107. Epub 2013 Feb, 20. PMID:23430154 doi:https://dx.doi.org/10.1093/nar/gkt107
↑ Ahlquist P. RNA-dependent RNA polymerases, viruses, and RNA silencing. Science. 2002 May 17;296(5571):1270-3. PMID:12016304 doi:https://dx.doi.org/10.1126/science.1069132
↑ Fukushi S, Kojima S, Takai R, Hoshino FB, Oka T, Takeda N, Katayama K, Kageyama T. Poly(A)- and primer-independent RNA polymerase of Norovirus. J Virol. 2004 Apr;78(8):3889-96. PMID:15047805

3D Structures of RNA polymerase

Updated on 21-October-2018

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 α
- 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
- 3ef0, 3ef1 - SpRNAP II subunit α C terminal – Schizosaccharomyces pombe
- 3h0g – SpRNAP II
- 3ayh - SpRNAP III subunit Rpc8+Rpc9
- 4kbj – MtuRNAP β subunit – Mycobacterium tuberculosis
- 5uh7 - MtuRNAP subunit β’
- 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 β – 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
- 3nff, 3nfg, 3nfh, 3nfi – RNAP I fragments (mutant) – Candida glabrata
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 - EcRNAP subunits α,β,β’,ω + RNA + DNA – 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
- 5tbz - EcRNAP subunits α,β,β’ + NusG – Cryo EM
- 6fbv - MtuRNAP subunits α,β,β’,ω + σ factor – single particle EM
- 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
Prokaryotic DNA-dependent RNAP complex with protein + DNA/RNA
- 3aoh, 3aoi - TtRNAP subunits α,β,β’,ω + DNA + RNA + GFH1
- 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 - TtRNAP subunits α,β,β’,ω + σ factor + DNA
- 4q5s, 5d4c, 5e17, 5e18, 5vo8 - 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
- 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
- 5nsr, 5nss, 6gh6, 6gh5, 6ca0 - 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
- 3iyd - EcRNAP subunits α,β,β’,ω + σ factor + catabolite gene activator + DNA
- 4s20 - EcRNAP subunits α,β,β’,ω + σ factor + RAPA + DNA
- 6c6u - EcRNAP subunits α,β,β’,ω + NusG + DNA – Cryo EM
- 6c6t, 6c6s - EcRNAP subunits α,β,β’,ω + RFAH + DNA – Cryo EM
- 5ms0 - EcRNAP subunits α,β,β’,ω + σ factor + NusB + NusG + NusA + 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
- 5uha - MtuRNAP subunits α,β,β’,ω + σ factor + DNA
- 5uh9, 5uh8 - 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 small molecule
- 1zyr, 2a68, 2a69, 2a6e, 2a6h - TtRNAP subunits α,β,β’,ω + antibiotic
- 1i6v, 1ynj, 1ynn - TaRNAP subunits α,β,β’,ω + antibiotic
Eukaryotic DNA-dependent RNAP I
- 1a1d – yRNAP subunit RPB8 – yeast - NMR
- 2rf4 - yRNAP I subunit RPA4
- 5g5l, 5lmx, 5m3f, 5m3m, 5m5w, 5m5x, 5m5y, 5m64 – yRNAP I – Cryo EM
- 5n5y, 5n5z, 5n60, 5oa1 – yRNAP I + RRN – Cryo EM
- 5n61, 6h68, 6h67 – yRNAP I + RRN + DNA + RNA – Cryo EM
- 5w66, 5w65, 5w64, 5w5y – yRNAP I + transcription initiation factor + DNA + RNA – Cryo EM
Eukaryotic DNA-dependent RNAP II
- 1qkl - hRNAP II subunit RPB6 - human
- 2c35 - hRNAP II subunits RPB4 RPB7 (mutant) – NMR
- 2f3i - hRNAP II subunits RPB8 RPB17 RPABC3 – NMR
- 2ghq, 2ght - hRNAP II subunits RPB1 + hRNAP II C terminal
- 2q5e, 3l0b, 3l0c - hRNAP II C terminal
- 1nik, 1nt9, 1wcm, 2b8k, 3fki, 3qt1, 1i3q, 1i50, 1dzf, 5ip7, 5ip9, 5u5q – yRNAP II
- 4x67, 4x6a, 4y52, 4y7n, 5c3e, 5c44, 5c4a, 5c4j, 5c4x, 6bqf, 6bm4, 6bm2, 6blp, 6blo, 5w51, 5w4u – yRNAP II + DNA + RNA
- 6a5v, 6a5u, 6a5t, 6a5r, 6a5p, 6a5o, 6a6l – yRNAP II + DNA + RNA + histones – Cryo EM
- 3j1n, 4v1n, 5fmf, 5x51, 5x50, 5x4z – yRNAP II – Cryo EM
- 1y14 - yRNAP II subunits RPB4 RPB7
- 5flm – bRNAP II + DNA + RNA - bovine
- 5oik – bRNAP II + SPT4 + SPT5 + DNA + RNA
- 3ef0, 3ef1 - fyRNAP II subunit α C terminal – fission yeast
- 3h0g – fyRNAP II
- 5u0s – fyRNAP II + mediator complex – Cryo EM
Eukaryotic DNA-dependent RNAP II complex with DNA/RNA
- 4boc – hRNAP + DNA
- 1i6h, 4a3i - yRNAP II + DNA
- 4v1m - yRNAP II + DNA – Cryo EM
- 1r9s, 2ja5, 2ja6, 2ja7, 2ja8, 2nvq, 2nvt, 2nvx, 2nvy, 2nvz, 3gtg, 3gtj, 3gtk, 3gtl, 3gtm, 3gto, 3gtp, 3gtq, 3hov, 3how, 3hox, 3hoy, 3hoz, 3po2, 3po3, 3m3y, 3m4o, 4a3g, 4a93, 4a3b, 4a3c, 4a3d, 4a3e, 4a3f, 4a3j, 4a3k, 4a3l, 4a3m - yRNAP II + RNA + DNA
- 5vvs - yRNAP II + RNA + DNA – Cryo EM
- 1y1w, 1y77, 2r7z, 2r92, 2r93, 3h3v, 3rzd, 3rzo, 3s15, 3s16, 3s17, 3s1m, 3s1n, 3s1q, 3s1r, 3s2d, 3s2h - yRNAP II + RNA
- 2b63 - yRNAP II + nucleotide + RNA
- 2e2i, 2e2j - yRNAP II + nucleotide + DNA
- 2yu9, 3i4m, 3i4n - yRNAP II + nucleotide + DNA + RNA
- 2vum - yRNAP II + inhibitor + 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
- 3pgl - hRNAP II C terminal + inhibitor
- 3cqz, 1k83 - yRNAP II + inhibitor
- 1twa, 1twc, 1twf, 1twg, 1twh - yRNAP II + nucleotide
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 μ
- 4lzd – hRNAP μ
- 4lzg, 4m04, 4m0a, 5twp, 5twq, 5twr, 5tws. 5txx, 5txz, 5tyb, 5tyc, 5tyd, 5tye, 5tyf, 5tyg, 5tyu, 5tyv, 5tyw, 5tyx, 5tyy, 5tyz – hRNAP μ + DNA
- 5vzi, 5vzh, 5vzg, 5vzf, 5vze, 5vzd, 5vzc, 5vzb, 5vza, 5vz9, 5vz8, 5vz7 – hRNAP μ (mutant) + DNA + nucleotide
Eukaryotic DNA-dependent RNAP mitochondrial
- 4boc – hRNAP + DNA
- 6erq, 6erp – hRNAP + DNA + MTTFA + dimethyladenosine transferase
- 3spa - hRNAP + polypeptide
Eukaryotic DNA primase
- 4lik, 4mhk - 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 - yDNAP large subunit
Eukaryotic DNA primase complex
- 4lil - hDNAP small subunit + UTP
- 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
- 5vaz – dnaG – Pseudomonas aeruginosa
- 4im9 – VcdnaG C-terminal
- 3m1m – DNAP RNA polymerase domain – Sulfolobus islandicus
- 1zt2, 2pa8, 2pmz, 3hkz - DNAP small + large subunit – Sulfolobus solfataricus
- 2au3 – DNAP zinc-binding and RNA polymerase 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 – Geobacillus stearothermophilus
- 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
RNA polymerase from Bacteriophage T7
- 1q57 – T7DNAP/helicase (mutant) – Enterobacteria phage T7
- 1nui – T7DNAP/helicase primase fragment (mutant)
- 1cr0 - T7DNAP/helicase helicase domain
- 1cr1, 1cr2, 1cr4 - T7DNAP/helicase helicase domain + nucleotide
- 4rnp – T7RNAP
- 1aro – T7RNAP + T7 lysozyme
- 1cez, 1h38, 1qln, 2pi4, 2pi5 - T7RNAP + DNA
- 1msw, 1s0v, 1s76, 1s77, 3e2e, 3e3j - T7RNAP + DNA + RNA
RNA-dependent RNAP
- 3phu, 1khv, 1khw – HfRNAP L RNA-directed – Hemorrhagic fever virus
- 5v5i, 5v5h, 5v5g – HfRNAP L + ubiquitin
- 2xwh, 2xxd, 2xhu,2xhw, 3i5k, 1c2p, 1csj, 1quv, 1yuy, 1yv2, 1yvx, 1yvz, 3gsz, 4aep, 4aex, 2wrm, 3mwv, 3mww – HvRNAP Ns5b domain – Hepatitis virus
- 3vc8 - HvRNAP cytoplasmic domain C terminal
- 3vcb, 4ry4, 4ry5, 4ry6, 4ry7 - HvRNAP cytoplasmic domain C terminal (mutant)
- 2xym, 2xhv, 2xi2, 4e76, 4adp, 4obc, 4wt9 - HvRNAP Ns5b domain (mutant)
- 1rdr - PoRNAP – Polio virus
- 1tql, 2ijd, 2ijf, 4nlo, 4nlp, 4nlq, 4nlr, 4nls, 4nlt, 4nlu, 4nlv, 4nlw, 4nlx, 4nly, 4r0e - PoRNAP (mutant)
- 2xi5, 2xi7 – BvRNAP L N-terminal – Bunyavirus
- 3jsb – RNAP (mutant) – Lymphocytic choriomengitis virus
- 2wk4, 2uut, 2uuw – SvRNAP (mutant) – Sapporo virus
- 2ckw - SvRNAP residues 1135-1649
- 3nky, 4wyl, 4wyw, 6gvv - FmRNAP (mutant) - Foot-and-mouth virus
- 1hhs, 4a8o, 4b02, 1hi8, 5fj6 – P6RNAP – Bacteriophage φ-6
- 2jl9, 2jlf, 1wac – P6RNAP (mutant)
- 5fj7 – P6RNAP + major inner protein P1
- 2po4 – N4RNAP polymerase domain – Bacteriophage N4
- 1l9k – DevRNAP N terminal – Dengue virus
- 2j7u, 4c11 - DevRNAP polymerase domain
- 5ccv - DevRNAP NS5
- 1oks – RNAP α subunit – Measles virus
- 1r4g - RNAP α subunit – Sendai virus – NMR
- 1s48, 1s49, 1s4f – DvRNAP residues 71-679 – Diarrhea virus
- 2cjq - DvRNAP polymerase domain
- 1sh0, 1sh2, 1sh3 - NvRNAP C terminal – Norwalk virus
- 1vyi - RNAP α subunit C terminal – Rabies virus
- 2hcn, 2hcs, 2hfz – RNAP polymerase domain – West Nile virus
- 2pgg, 2pus – RNAP – Bursal disease virus
- 2r7o, 2r7q – SrRNAP – Simian rotavirus
- 4au6 - RNAP – bovine rotavirus – Cryo-EM
- 2yi8, 2yi9, 2yia, 2yib – IpnvRNAP – Infectious pancreatic necrosis virus
- 3n6l – EvRNAP – Human enterovirus
- 4uci, 4ucj, 4ucl, 4ucy, 4ucz – HmpvRNAP residues 1600-2005 – Human metapneumovirus
- 4uck, 4ud0 – HmpvRNAP residues 1600-2005 (mutant)
- 4zp8, 4zp9, 4zpa, 4zpb, 4zpc, 4zpd – CvRNAP residues 1724-2185 (mutant) – Coxsackievirus
- 3ddk – CvRNAP residues 1724-2185
- 3nah, 3nai, 3qid, 3uqs – MnvRNAP – Murine norovirus
- 4wfx, 4wfy, 4wfz – CvRNAP RDRP domain (mutant)
- 2j7n, 2j7o – RNAP residues 381-1402 – Neurospora crassa
- 4gzk, 4ieg – RNAP – cystovirus 12
- 4i1t – RNAP L – Pichinde virus
- 5chs – RNAP L N-terminal – Vescicular stomatitis Indiana virus
- 4xha, 4xhi – TavRNAP – Thosea asigna virus
- 4miw, 5izh, 5j1n, 5j1p – RNAP L N terminal – Lassa virus
- 4mtp – RNAP RDRP module – Encephalitis virus
- 4cgx, 4chc – TvRNAP N terminal – Thogoto virus
- 4chd – TvRNAP 627 domain
- 4che, 4chf – TvRNAP cap-binding domain
- 5fsw - NvRNAP C terminal – Thielavia terrestris
- 5hsb – RNAP – Andes virus
- 5ize – RNAP L – Hantaan virus
- 5ltf – LcmvRNAP L – Lymphocytic choriomeningitis mammarenavirus
- 5lts - LcmvRNAP (mutant)
- 5u0c - ZvRNAP NS5 – Zika virus
RNA-dependent RNAP complex with RNA
- 4e78, 4e7a, 4wta, 4wtc, 4wtd, 4wte, 4wtf, 4wtg, 4wti, 4wtj, 4wtk, 4wtl, 4wtm - HvRNAP Ns5b domain (mutant) + RNA
- 3ol6, 2jlg, 4k4s, 4k4t, 4k4u, 4k4v, 4k4w – PoRNAP (mutant) + RNA
- 3ol7, 3ol8, 3ol9, 3ola, 3olb - PoRNAP (mutant) + RNA + nucleotide
- 3klv, 3kmq, 3kms, 3kna, 3nl0, 3nma, 4iqx, 4wzm, 4wzq, 4x2b, 5jxs – FmRNAP (mutant) + RNA
- 3koa - FmRNAP (mutant) + RNA + nucleotide
- 1wne – FmRNAP + RNA
- 2e9r, 2e9t, 2e9z, 2ec0 - FmRNAP + RNA + inhibitor
- 1uvi, 1uvl, 1uvm, 1uvn, 4a8f, 4a8k, 4a8m, 4a8q, 4a8s, 4a8w, [[4a8y – P6RNAP + RNA
- [[3bsn, 3bso, 3h5x, 3h5y - NvRNAP + RNA + nucleotide
- 2r7r, 2r7s, 2r7t, 2r7u, 2r7v, 2r7w, 2r7x – SrRNAP + RNA
- 5amq, 5amr – BvRNAP + RNA
- 4k50 – RNAP + RNA – Human rhinovirus
- 3c2p, 3c3l, 3c46, 3q0a - N4RNAP polymerase domain + promoter DNA
- 1hht, 1hi0 – P6RNAP + DNA
- 1uvj, 1uvk – P6RNAP + RNA
- 4k4x, 4k4y, 4k4z – CvRNAP + RNA
RNA-dependent RNAP complex with protein
- 3phw, 2pt2, 3pt2 – HfRNAP + ubiquitin
- 3phx, 3pse – HfRNAP + ISG15
- 2d7s, 2f8e – FmRNAP + VPG
- 5y3d – MnvRNAP + VPG
- 3cdw - CvRNAP + POP + VPG
- 4f5x – SrRNAP + Vp2 + Vp6
- 5h0r – RNAP + Vp4 + RNA - BMCPV
- 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
RNA-dependent RNAP complex with small molecule
- 2xwy, 3mf5, 3hkw, 3hky, 3lkh, 3gnv, 3gnw, 3h98, 3g86, 3h59, 1nhu, 1nhv, 2brk, 2brl, 2gc8, 2giq, 2gir]], 2hai, 2hwh, 2hwi, 2i1r, 2ijn, 2jc0, 2jc1, 2qe2, 2qe5, 2wcx, 2who, 3ciz, 3cj0, 3cj2, 3cj3, 3cj4, 3cj5, 3cso, 3cvk, 3fqk, 3fql, 3gol, 3h5s, 3h5u, 3q0z, 3qgd, 3qge, 3qgf, 3qgg, 3qgh, 3qgi, 3ska, 3ske, 3skh, 3uph]], 3upi, 4dru, 3vqs, 3udl, 4eo6, 4eo8, 4eaw, 4gmc, 4ih5, 4ih6, 4ih7, 4iz0, 4jtz, 4jtw, 4jty, 4ju1, 4ju2, 4jjs, 4jju, 4j02, 4j04, 4j06, 4j08, 2yoj, 3tuq, 3tuv, 3u4o, 3u4r, 4mk7, 4mk8, 4mk9, 4mka, 4mkb, 4mz4, 4nld, 3tyq, 3tyv, 4mia, 4mib, 4oow, 4tlr, 5pzk, 5pzl, 5pzm, 5pzn, 5pzo, 5pzp, 5trh, 5tri, 5trj - HvRNAP Ns5b domain + inhibitor
- 3gyn, 1os5, 3br9, 3bsa, 3bsc, 3cde, 3co9, 3cwj, 3d28, 3d5m, 3e51, 3frz, 3igv, 3hvo, 3h2l, 4kai, 4kb7, 4kbi, 4ke5, 4khm, 4khr, 5twm, 5twn - HvRNAP Ns5b domain (mutant) + inhibitor
- 2xi3 - HvRNAP Ns5b domain (mutant) + nucleotide
- 1gx5, 1gx6 - HvRNAP Ns5b domain + nucleotide
- 2im1, 2im0, 2im2, 2im3, 2ily, 2ilz - PoRNAP (mutant) + nucleotide
- 3n6m, 3n6n – EvRNAP + nucleotide
- 3sfg – MnvRNAP + thio-uridine
- 3sfu – MnvRNAP + ribavirine
- 3upf, 3ur0, 4nru, 4o4r – MnvRNAP + inhibitor
- 4lq3, 4lq9 – RNAP + inhibitor – human norovirus
- 3cdu– CvRNAP + POP
- 3eva, 3evb, 3evc, 3evd, 3eve, 3evf, 3evg – RNAP N terminal + nucleotide – Yellow fever virus
- 1hi1 – P6RNAP + nucleotide
- 5cx6, 5cyr - TavRNAP + nucleotide
- 5hmw, 5f3t, 5hmx, 5hmy, 5hn0, 5hmz, 5iq6, 5k5m - DevRNAP Ns5 + inhibitor
- 5ehg - DevRNAP NS5 + SAM + inhibitor
- 5goz, 5gp1 - ZvRNAP NS5 + SAH + GTP
- 5ltn, 5t2t - LcmvRNAP + inhibitor
Influenza virus polymerase acidic protein (or PA or subunit P2)
- 3hw3, 3hw4, 3hw5 - IvRNAP PA (mutant) + Mn + nucleotide – Influenza virus
- 3hw6, 6fsb - IvRNAP PA (mutant) + Mn
- 3wi0 – IvRNAP PA (mutant)
- 4w9s, 5fdd, 5fdg, 5i13, 5ieq, 5if2, 5if5, 5if7, 5if8, 5ifb, 5ifc, 5ifd, 5wa6, 5wa7, 5wb3, 5wap, 5w9g, 5w92, 5w44, 5v0u – IvRNAP PA + inhibitor
- 5wg9, 5wfz, 5wfw, 5wfm, 5wf3, 5wei, 5wef, 5web, 5we9, 5we7, 5wdw, 5wdn, 5wdc, 5wct, 5wcs, 5w73, 5w7u, 5w3i, 5vrj, 5vqn, 5vpx, 5vpt, 5vp8 – IvRNAP PA (mutant) + inhibitor
- 3cm8 – IvRNAP PA + RNA-directed RNA polymerase PA peptide
- 4wrt, 4wsa – IvRNAP PA + PB2 + RNA-directed RNA polymerase PA + RNA
- 4e5e, 4zqq, 5jht, 5jhv – IvRNAP PA residues 1-50, 73-196 + Mn
- 4e5f, 4e5g, 4e5h, 4e5i, 4e5j, 4e5l, 4yyl, 4zhz, 4zi0, 6fs7, 6fs6 – IvRNAP PA residues 1-50, 73-196 + Mn + inhibitor
- 6fs8 – IvRNAP PA residues 1-196 + Mn + inhibitor
- 6fs9 – IvRNAP PA residues 1-196 (mutant) + Mn + inhibitor
- 3ebj, 2w69 - IvRNAP PA residues 1-256
- 4iuj - IvRNAP PA residues 254-713
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
- 3cw4 - IvRNAP PB2 627 + NLS domains
- 2gmo - IvRNAP PB2 627 + NLS domains - NMR
- 4eqk, 5efa, 5efc – IvRNAP PB2 cap-binding domain + nucleotide
- 4nce, 3wi1 – IvRNAP PB2 cap-binding domain (mutant) + nucleotide
- 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
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
- 4wsb, 5fmz, 5m3h, 5m3j, 5msg, 6f5o, 6evj - IvRNAP PB1 + IvRNAP PA + IvRNAP PB2 + RNA
- 6evk - IvRNAP PB1 + IvRNAP PA + IvRNAP PB2 + RNA + GTP
- 5d98, 5d9a - IvRNAP PB1 + IvRNAP PA + IvRNAP PB2
- 6f5p - IvRNAP PB1 + IvRNAP PA + IvRNAP PB2 + polyAla
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) + nucleotide
- 4zrl – CeRNAP gld-2 + germline development defective 3 – Caenorhabidis elegans
- 5jnb – CeRNAP gld-2 (mutant) + RNP-8

References

Created with the participation of Craig T Martin.

Proteopedia Page Contributors and Editors (what is this?)

Alexander Berchansky, Karsten Theis, Joel L. Sussman, Michal Harel

[1] Cramer P, Armache KJ, Baumli S, Benkert S, Brueckner F, Buchen C, Damsma GE, Dengl S, Geiger SR, Jasiak AJ, Jawhari A, Jennebach S, Kamenski T, Kettenberger H, Kuhn CD, Lehmann E, Leike K, Sydow JF, Vannini A. Structure of eukaryotic RNA polymerases. Annu Rev Biophys. 2008;37:337-52. doi: 10.1146/annurev.biophys.37.032807.130008. PMID:18573085 doi:https://dx.doi.org/10.1146/annurev.biophys.37.032807.130008

[2] Comai L. Mechanism of RNA polymerase I transcription. Adv Protein Chem. 2004;67:123-55. PMID:14969726 doi:https://dx.doi.org/10.1016/S0065-3233(04)67005-7

[3] Hahn S. Structure and mechanism of the RNA polymerase II transcription machinery. Nat Struct Mol Biol. 2004 May;11(5):394-403. PMID:15114340 doi:https://dx.doi.org/10.1038/nsmb763

[4] Longo DL, Herbert V. Radioassay for serum and red cell folate. J Lab Clin Med. 1976 Jan;87(1):138-51. PMID:1452

[5] Frick DN, Richardson CC. DNA primases. Annu Rev Biochem. 2001;70:39-80. PMID:11395402 doi:https://dx.doi.org/10.1146/annurev.biochem.70.1.39

[6] Naue N, Beerbaum M, Bogutzki A, Schmieder P, Curth U. The helicase-binding domain of Escherichia coli DnaG primase interacts with the highly conserved C-terminal region of single-stranded DNA-binding protein. Nucleic Acids Res. 2013 Apr;41(8):4507-17. doi: 10.1093/nar/gkt107. Epub 2013 Feb, 20. PMID:23430154 doi:https://dx.doi.org/10.1093/nar/gkt107

[7] Ahlquist P. RNA-dependent RNA polymerases, viruses, and RNA silencing. Science. 2002 May 17;296(5571):1270-3. PMID:12016304 doi:https://dx.doi.org/10.1126/science.1069132

[8] Fukushi S, Kojima S, Takai R, Hoshino FB, Oka T, Takeda N, Katayama K, Kageyama T. Poly(A)- and primer-independent RNA polymerase of Norovirus. J Virol. 2004 Apr;78(8):3889-96. PMID:15047805

[1]

[2]

[3]

[4]

[5]

[6]

[7]

[8]

@@ Line 61: / Line 61: @@
 **[[1xpp]] – RNAP subunit L – ''Thermoplasma acidophilum'' <br />
 **[[2waq]], [[2wb1]], [[4ayb]] – SsRNAP <br />
-**[[3e7h]] – RNAP subunit β – ''Vibrio cholera''<br />
+**[[3e7h]] – VcRNAP subunit β – ''Vibrio cholera''<br />
 **[[1ef4]] – MtRNAP subunit RPB10 – ''Methanothermobacter thermautotrophicus''<br />
 **[[1eik]] - MtRNAP subunit RPB5 – NMR<br />
@@ Line 242: / Line 242: @@
 **[[3spa]] - hRNAP  + polypeptide <br />
+*''Eukaryotic DNA primase''
+**[[4lik]], [[4mhk]] - hDNAP small subunit<br />
-*''DNA primase''
-**[[4lik]] - hDNAP small subunit<br />
-**[[4lil]] - hDNAP small subunit + UTP<br />
 **[[3q36]] – hDNAP large subunit<br />
 **[[5i7m]] – hDNAP large subunit (mutant)<br />
+**[[3l9q]] – hDNAP large subunit P58C domain <br />
+**[[5dqo]] – hDNAP large subunit P58C domain (mutant)<br />
+**[[4rr2]] - hDNAP small + large subunit<br />
 **[[4bpu]] - hDNAP small (mutant) + large subunit<br />
-**[[4bpw]] - hDNAP small (mutant) + large subunit + UTP<br />
-**[[4bpx]] - hDNAP small (mutant) + DNA polymerase α subunit<br />
 **[[4ehs]] – HpDNAP C terminal<br />
-**[[4lim]] - yDNAP small subunit<br />
+**[[4lim]], [[4mm2]] - yDNAP small subunit<br />
 **[[3lgb]] - yDNAP large subunit<br />
-*''Bacterial primase''
+*''Eukaryotic DNA primase complex''
+**[[4lil]] - hDNAP small subunit + UTP<br />
+**[[5f0s]], [[5f0q]] – hDNAP large subunit C terminal + RNA<br />
+**[[4bpw]] - hDNAP small (mutant) + large subunit + UTP<br />
+**[[4bpx]] - hDNAP small (mutant) + DNA polymerase α catalytic subunit<br />
+**[[5exr]] - hDNAP small + large subunits + DNA polymerase α catalytic subunit<br />
+*''Bacterial DNA primase''
-**[[2r6a]], [[2r6c]] - GsdnaG helicase binding domain + helicase – ''Geobacillus stearothermophilus''<br />
+**[[1d0q]] - GsDNAP zinc-binding domain - ''Geobacillus stearothermophilus''<br />
-**[[4m4w]] - GsdnaG helicase binding domain + helicase + DnaI<br />
-**[[1d0q]] - GsDNAP zinc-binding domain<br />
 **[[1z8s]] - GsdnaG dnaB binding domain - NMR<br />
 **[[2haj]] - EcdnaG catalytic domain - NMR<br />
-**[[3b39]] – EcdnaG catalytic domain + DNA<br />
 **[[1t3w]] – EcdnaG C-terminal<br />
 **[[1eqn]], [[1dd9]], [[1dde]] – EcdnaG catalytic core<br />
 **[[5w33]] - MtudnaG <br />
-**[[5w36]], [[5w35]], [[5w34]] - MtudnaG + DNA<br />
 **[[5vaz]] – dnaG – ''Pseudomonas aeruginosa'' <br />
+**[[4im9]] – VcdnaG C-terminal<br />
 **[[3m1m]] – DNAP RNA polymerase domain – ''Sulfolobus islandicus''<br />
 **[[1zt2]], [[2pa8]], [[2pmz]], [[3hkz]]  - DNAP small + large subunit – ''Sulfolobus solfataricus''<br />
 **[[2au3]] – DNAP zinc-binding and RNA polymerase domains – ''Aquifex aeolicus''<br />
 **[[1v33]] - PhDNAP small subunit – ''Pyrocuccus horikoshii''<br />
-**[[1v34]] - PhDNAP small subunit + nucleotide<br />
 **[[1g71]] - PfDNAP small subunit<br />
 **[[4e2k]] – SaDNAP – ''Staphylococcus aureus''<br />
-**[[2lzn]] – SaDNAP C terminal – NMR<br />
+**[[2lzn]] – SaDNAP C-terminal – NMR<br />
-**[[4edg]], [[4edk]], [[4edr]], [[4edt]], [[4edv]], [[4ee1]] – SaDNAP + nucleotide
+**[[5guj]] – BsdnaG RNAP domain <br />
+*''Bacterial DNA primase complex''
+**[[2r6a]], [[2r6c]] - GsdnaG helicase binding domain + helicase – ''Geobacillus stearothermophilus''<br />
+**[[4m4w]] - GsdnaG helicase binding domain + helicase + DnaI<br />
+**[[3b39]] – EcdnaG catalytic domain + DNA<br />
+**[[5w36]], [[5w35]], [[5w34]] - MtudnaG + DNA<br />
+**[[1v34]] - PhDNAP small subunit + UTP<br />
+**[[4edg]], [[4edk]], [[4edr]], [[4edt]], [[4edv]], [[4ee1]] – SaDNAP + nucleotide<br />
 *''RNA polymerase from Bacteriophage T7''

RNA polymerase: Difference between revisions

Revision as of 10:04, 21 October 2018

3D Structures of RNA polymerase

References

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools