RNA polymerase

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{{STRUCTURE_3m3y| PDB=3m3y | SIZE=400| SCENE=RNA_polymerase/Cv/1 |right|CAPTION=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). }}
{{STRUCTURE_3m3y| PDB=3m3y | SIZE=400| SCENE=RNA_polymerase/Cv/1 |right|CAPTION=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). }}
-
'''RNA polymerase''' (RNAP, '''DNA primase''', dnaG) catalyzes the addition of nucleotides to RNA during transcription. DNA primase (DNAP) is RNAP which catalyzes the synthesis of the RNA primer which complements an ssDNA template and initiates DNA synthesis. dnaG is a bacterial primase. Polymerase acidic protein (PAP) is an Influenza virus RNA polymerase. It is implicated in endonuclease cleavage of RNA primers. <scene name='1qln/Rockets_steitz_colors/1'>View of the nucleic acid</scene> ([[1qln]]; blue: nontemplate strand; cyan: template strand; red:RNA). See also [[Transcription and RNA Processing]].<br />
+
'''RNA polymerase''' (RNAP, '''DNA primase''', dnaG) catalyzes the addition of nucleotides to RNA during transcription. DNA primase (DNAP) is RNAP which catalyzes the synthesis of the RNA primer which complements an ssDNA template and initiates DNA synthesis. dnaG is a bacterial primase. '''Influenza virus RNA polymerase''' 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. <scene name='1qln/Rockets_steitz_colors/1'>View of the nucleic acid</scene> ([[1qln]]; blue: nontemplate strand; cyan: template strand; red:RNA). See also [[Transcription and RNA Processing]].<br />
For RNA polymerase from bacteriophage T7 see<br />
For RNA polymerase from bacteriophage T7 see<br />
* [[Molecular Playground/T7 RNAP Conformations]]<br />
* [[Molecular Playground/T7 RNAP Conformations]]<br />
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{{#tree:id=OrganizedByTopic|openlevels=0|
{{#tree:id=OrganizedByTopic|openlevels=0|
-
*DNA-dependent RNA polymerase
+
*Prokaryotic DNA-dependent RNAP
-
**[[2y0s]] – SsRNAP – ''Sulfolobus shibata''<br />
+
**[[2y0s]] – SsRNAP – Sulfolobus shibata<br />
-
**[[4b1p]] – SsRNAP + DNA<br />
+
**[[1ryq]] - PfRNAP subunit ε’’ - Pyrococcus furiosus<br />
-
**[[3q22]], [[3q23]], [[3q24]], [[4ff1]], [[4ff2]], [[4ff3]], [[4ff4]] – RNAP + DNA – Enterobacteria phage N4<br />
+
**[[1go3]] – MjRNAP subunit RPB4, RPB7 - Methanocaldococcus jannaschii<br />
-
**[[3p8b]] – PfRNAP subunit ε’’ + transcription antitermination protein – ''Pyrococcus furiosus''<br />
+
**[[1iw7]], [[1smy]] - TtRNAP subunits α,β,β’,ω − Thermus thermophilus<br />
-
**[[3qqc]] - PfRNAP subunits β,ε’’ + transcription antitermination protein<br />
+
**[[1doq]] - TtRNAP subunit α<br />
-
**[[1ryq]] - PfRNAP subunit ε’’<br />
+
**[[3lti]]– EcRNAP subunit β fragment – Escherichia coli<br />
-
**[[3lpe]] - MjRNAP subunit ε’’ + transcription antitermination protein – ''Methanocaldococcus jannaschii''<br />
+
**[[4iqz]] - EcRNAP subunit β’ <br />
-
**[[1go3]] – MjRNAP subunit RPB4, RPB7<br />
+
**[[3k4g]], [[1coo]] - EcRNAP subunit α<br />
-
**[[3aoh]], [[3aoi]] - TtRNAP subunits α,β,β’,ω + DNA +RNA + GFH1 – ''Thermus thermophilus''<br />
+
**[[1bdf]] - EcRNAP subunit α (mutant) <br />
 +
**[[3lu0]] - EcRNAP subunits α,β,β’,ω – Electron diffraction<br />
 +
 
 +
**[[2krc]] - BsRNAP subunit δ N-terminal – Bacillus subtilis – NMR<br />
 +
**[[2ly7]] - BsRNAP subunit β − NMR<br />
 +
**[[2m4k]] - BsRNAP subunit δ − NMR<br />
 +
**[[4nc7]], [[4nc8]] - BsRNAP subunit δ <br />
 +
**[[2max]] - HpRNAP subunit α − Helicobacter pylori - NMR<br />
 +
**[[1qyp]] – RNAP II C terminal – Thermococcus celer – NMR<br />
 +
**[[3ef0]], [[3ef1]] - SpRNAP II subunit α C terminal – Schizosaccharomyces pombe<br />
 +
**[[3h0g]] – SpRNAP II<br />
 +
**[[3ayh]] - SpRNAP III subunit Rpc8+Rpc9<br />
 +
**[[4kbj]] – RNAP β subunit – Mycobacterium tuberculosis<br />
 +
**[[4noi]] – RNAP α subunit – Campylobacter jejuni<br />
 +
**[[1hqm]] – TaRNAP subunits α,β,β’,ω − Thermus aquaticus<br />
 +
**[[2gho]] - TaRNAP subunits α,β,β’ <br />
 +
**[[2auj]], [[2auk]] - TaRNAP subunit β’ <br />
 +
**[[1xpp]] – RNAP subunit L – Thermoplasma acidophilum <br />
 +
**[[2waq]], [[2wb1]], [[4ayb]] – SsRNAP <br />
 +
**[[3e7h]] – RNAP subunit β – Vibrio cholera<br />
 +
**[[1ef4]] – MtRNAP subunit RPB10 – Methanothermobacter thermautotrophicus<br />
 +
**[[1eik]] - MtRNAP subunit RPB5 – NMR<br />
 +
**[[4qiw]] – TkRNAP subunits a’’+d+e’+f+h+k+l+n+p – Thermococcus kodakarensis<br />
 +
**[[4qjf]] - TkRNAP subunits e’+f <br />
 +
**[[4qjv]] - TkRNAP subunits d+l<br />
 +
 
 +
*Prokaryotic DNA-dependent RNAP complex with DNA/RNA
 +
 
 +
**[[4b1p]], [[4b1o]] – SsRNAP + DNA<br />
 +
**[[3q22]], 3q23]], [[3q24]], [[4ff1]], [[4ff2]], [[4ff3]], [[4ff4]] – RNAP + DNA – Enterobacteria phage N4<br />
**[[2o5i]], [[2o5j]], [[4gzy]], [[4gzz]] - TtRNAP subunits α,β,β’,ω + DNA +RNA<br />
**[[2o5i]], [[2o5j]], [[4gzy]], [[4gzz]] - TtRNAP subunits α,β,β’,ω + DNA +RNA<br />
-
**[[1iw7]], [[1smy]] - TtRNAP subunits α,β,β’,ω<br />
+
**[[4wqs]] - TtRNAP subunits α,β,β’,ω + DNA<br />
-
**[[1zyr]], [[2a68]], [[2a69]], [[2a6e]], [[2a6h]] - TtRNAP subunits α,β,β’,ω + antibiotic<br />
+
**[[2ppb]] - TtRNAP subunits α,β,β’,ω + antibiotic + DNA + RNA + substrate analog<br />
**[[2ppb]] - TtRNAP subunits α,β,β’,ω + antibiotic + DNA + RNA + substrate analog<br />
-
**[[2be5]] - TtRNAP subunits α,β,β’,ω + σ factor + inhibitor<br />
+
**[[4igc]], [[4jk1]], [[4jk2]], [[4jkr]], [[4kmu]] - EcRNAP subunits α,β,β’,ω + RNA<br />
 +
**[[4kn4]], [[4kn7]] - EcRNAP subunits α,β,β’,ω + RNA + antibiotic<br />
 +
 
 +
*Prokaryotic DNA-dependent RNAP complex with protein
 +
 
 +
**[[3p8b]] – PfRNAP subunit ε’’ + transcription antitermination protein <br />
 +
**[[3qqc]] - PfRNAP subunits β, ε’’ + transcription antitermination protein<br />
 +
**[[3aoh]], [[3aoi]] - TtRNAP subunits α,β,β’,ω + DNA +RNA + GFH1<br />
 +
**[[2be5]]- TtRNAP subunits α,β,β’,ω + σ factor + inhibitor <br />
**[[2cw0]] - TtRNAP subunits α,β,β’,ω + σ factor<br />
**[[2cw0]] - TtRNAP subunits α,β,β’,ω + σ factor<br />
-
**[[4g7h]], [[4g7o]], [[4g7z]] - TtRNAP subunits α,β,β’,ω + σ factor + DNA<br />
+
**[[3wod]] - TtRNAP subunits α,β,β’,ω + σ factor + GP39<br />
 +
**[[4mq9]] - TtRNAP subunits α,β,β’,ω + σ factor + GE23077<br />
 +
**[[4oin]], [[4oio]] - TtRNAP subunits α,β,β’,ω + σ factor + GE23077 + DNA<br />
 +
**[[4oip]] - TtRNAP subunits α,β,β’,ω + σ factor + GE23077 + DNA + nucleotide<br />
 +
**[[4oiq]], [[4oir]] - TtRNAP subunits α,β,β’,ω + σ factor + GE23077 + DNA + antibiotic<br />
 +
**[[4g7h]], [[4g7o]], [[4g7z]], [[4q4z]] - TtRNAP subunits α,β,β’,ω + σ factor + DNA<br />
 +
**[[4q5s]] - TtRNAP subunits α,β,β’,ω + σ factor + DNA + RNA<br />
**[[3dxj]], [[3eql]] - TtRNAP subunits α,β,β’,ω + σ factor + antibiotic<br />
**[[3dxj]], [[3eql]] - TtRNAP subunits α,β,β’,ω + σ factor + antibiotic<br />
-
**[[1doq]] - TtRNAP subunit α<br />
+
**[[4wqt]] - TtRNAP subunits α,β,β’,ω + RNA cleavage stimulating factor<br />
**[[3mlq]] - TtRNAP subunit β + transcription-repair coupling factor<br />
**[[3mlq]] - TtRNAP subunit β + transcription-repair coupling factor<br />
-
**[[3lti]] – EcRNAP subunit β fragment – ''Escherichia coli''<br />
+
**[[3woe]], [[3wof]] - TtRNAP subunit β + GP39<br />
-
**[[4iqz]] - EcRNAP subunit β’ <br />
+
**[[2lmc]] - EcRNAP subunit β + RNAP inhibitor <br />
**[[2lmc]] - EcRNAP subunit β + RNAP inhibitor <br />
**[[3mmp]] - EcRNAP subunit β + EF-TU<br />
**[[3mmp]] - EcRNAP subunit β + EF-TU<br />
**[[3t72]] - EcRNAP subunit β + Pho box DNA + PhoB<br />
**[[3t72]] - EcRNAP subunit β + Pho box DNA + PhoB<br />
-
**[[3k4g]], [[1coo]] - EcRNAP subunit α<br />
 
**[[1lb2]], [[3n4m]] - EcRNAP subunit α + DNA + CAP<br />
**[[1lb2]], [[3n4m]] - EcRNAP subunit α + DNA + CAP<br />
**[[1xs9]] - EcRNAP subunit α + DNA + MARA<br />
**[[1xs9]] - EcRNAP subunit α + DNA + MARA<br />
**[[3n97]] - EcRNAP subunit α C terminal + DNA + σ factor<br />
**[[3n97]] - EcRNAP subunit α C terminal + DNA + σ factor<br />
-
**[[1bdf]] - EcRNAP subunit α (mutant)<br />
+
**[[4ljz]], [[4lk1]], [[4mey]] - EcRNAP subunits α,β,β’,ω + RNAP sigma factor <br />
-
**[[3lu0]] - EcRNAP subunits α,β,β’,ω – Electron diffraction<br />
+
**[[4mex]] - EcRNAP subunits α,β,β’,ω + RNAP sigma factor + salinamide<br />
-
**[[4igc]], [[4jk1]], [[4jk2]], [[4jkr]], [[4kmu]] - EcRNAP subunits α,β,β’,ω + RNA<br />
+
-
**[[4kn4]], [[4kn7]] - EcRNAP subunits α,β,β’,ω + RNA + antibiotic<br />
+
-
**[[4ljz]], [[4lk1]] - EcRNAP subunits α,β,β’,ω + RNAP sigma factor <br />
+
**[[4lk0]], [[4llg]] - EcRNAP subunits α,β,β’,ω + RNAP sigma factor + RNAP inhibitor<br />
**[[4lk0]], [[4llg]] - EcRNAP subunits α,β,β’,ω + RNAP sigma factor + RNAP inhibitor<br />
**[[3iyd]] - EcRNAP subunits α,β,β’,ω + RNAP sigma factor + catabolite gene activator + DNA<br />
**[[3iyd]] - EcRNAP subunits α,β,β’,ω + RNAP sigma factor + catabolite gene activator + DNA<br />
-
**[[2l0i]] – yRNAP C-terminal + RTT103 – yeast – NMR<br />
+
**[[4s20]] - EcRNAP subunits α,β,β’,ω + RNAP sigma factor + RAPA + DNA<br />
-
**[[1a1d]] – yRNAP subunit RPB8 – NMR<br />
+
**[[3ihq]], [[1z3e]], [[3gfk]] - BsRNAP subunit α +regulatory protein SPX
-
**[[4a3g]], [[4a93]], [[4a3b]], [[4a3c]], [[4a3d]], [[4a3e]], [[4a3f]], [[4a3j]], [[4a3k]], [[4a3l]], [[4a3m]] – yRNAP II + RNA + DNA<br />
+
**[[1l9u]] - TaRNAP subunits α,β,β’,ω + σ factor<br />
-
**[[4bxx]], [[4bxz]], [[4by1]], [[4by7]] – yRNAP II + RNA + DNA + transcription factor Bye1<br />
+
**[[l9z]] - TaRNAP subunits α,β,β’,ω + σ factor + DNA<br />
-
**[[4c2m]], [[4c3h]], [[4c3i]], [[4c3j]] – yRNAP<br />
+
**[[2jzb]] – RNAP subunit α + NUSA transcription elongation factor – Yersinia pseudotuberculosis<br />
-
**[[4a3i]] – yRNAP II + DNA<br />
+
**[[3tbi]] - RNAP subunit β + GP33 – Enterobacteria phage T4<br />
-
**[[2krc]] - BsRNAP subunit δ N-terminal – ''Bacillus subtilis'' – NMR<br />
+
**[[3lpe ]]- MjRNAP subunit ε’’ + transcription antitermination protein<br />
-
**[[3ihq]], [[1z3e]], [[3gfk]] - BsRNAP subunit α +regulatory protein SPX<br />
+
-
**[[2ly7]] - BsRNAP subunit β − NMR<br />
+
-
**[[2m4k]] - BsRNAP subunit δ − NMR<br />
+
-
**[[2max]] - HpRNAP subunit α − ''Helicobacter pylori'' - NMR<br />
+
-
**[[1qyp]] – RNAP II C terminal – ''Thermococcus celer'' – NMR<br />
+
-
**[[3ef0]], [[3ef1]] - SpRNAP II subunit α C terminal – ''Schizosaccharomyces pombe''<br />
+
-
**[[3h0g]] – SpRNAP II<br />
+
-
**[[3ayh]] - SpRNAP III subunit Rpc8+Rpc9<br />
+
-
**[[4kbj]] – RNAP β subunit – ''Mycobacterium tuberculosis''<br />
+
-
**[[4noi]] – RNAP α subunit – ''Campylobacter jejuni''<br />
+
-
*Eukaryotic DNA-dependent RNA polymerase
+
*Prokaryotic DNA-dependent RNAP complex with small molecule
-
**[[3o2q]], [[3o2s]] – hRNAP II subunit α C-terminal + symplekin – human<br />
+
**[[1zyr]], [[2a68]], [[2a69]], [[2a6e]], [[2a6h]] - TtRNAP subunits α,β,β’,ω + antibiotic<br />
-
**[[1qkl]] - hRNAP II subunit RPB6<br />
+
**[[1i6v, [[1ynj]], [[1ynn]] - TaRNAP subunits α,β,β’,ω + antibiotic<br />
-
**[[3j0k]] – hRNAP II + TFIIF – Cryo EM<br />
+
 
 +
 
 +
 
 +
Eukaryotic DNA-dependent RNAP
 +
 
 +
**[[1qkl]] - hRNAP II subunit RPB6 - human<br />
**[[2c35]] - hRNAP II subunits RPB4 RPB7 (mutant) – NMR<br />
**[[2c35]] - hRNAP II subunits RPB4 RPB7 (mutant) – NMR<br />
**[[2f3i]] - hRNAP II subunits RPB8 RPB17 RPABC3 – NMR<br />
**[[2f3i]] - hRNAP II subunits RPB8 RPB17 RPABC3 – NMR<br />
**[[2ghq]], [[2ght]] - hRNAP II subunits RPB1 + hRNAP II C terminal<br />
**[[2ghq]], [[2ght]] - hRNAP II subunits RPB1 + hRNAP II C terminal<br />
**[[2q5e]], [[3l0b]], [[3l0c]] - hRNAP II C terminal<br />
**[[2q5e]], [[3l0b]], [[3l0c]] - hRNAP II C terminal<br />
-
**[[2lto]] - hRNAP II subunit RPB1 + Tudor domain containing protein 3<br />
 
-
**[[3pgl]] - hRNAP II C terminal + inhibitor<br />
 
**[[2xub]], [[2xv4]] - hRNAP III subunits RPC3<br />
**[[2xub]], [[2xv4]] - hRNAP III subunits RPC3<br />
**[[2dk8]] – RNAP III RPC34 domain - mouse – NMR<br />
**[[2dk8]] – RNAP III RPC34 domain - mouse – NMR<br />
**[[2dk5]] – hRNAP III winged helix domain (mutant) – NMR<br />
**[[2dk5]] – hRNAP III winged helix domain (mutant) – NMR<br />
**[[2yu3]] - hRNAP III winged helix domain<br />
**[[2yu3]] - hRNAP III winged helix domain<br />
-
**[[3spa]] - hRNAP + polypeptide<br />
+
 
-
**[[4boc]] – hRNAP + DNA<br />
+
**[[4lzd]] – hRNAP μ<br />
**[[4lzd]] – hRNAP μ<br />
-
**[[4lzg]], [[4m04]], [[4m0a]] – hRNAP μ + DNA<br />
+
**[[3nff]], [[3nfg]], [[3nfh]], [[3nfi]] – RNAP I fragments (mutant) – Candida glabrata<br />
-
**[[3nff]], [[3nfg]], [[3nfh]], [[3nfi]] – RNAP I fragments (mutant) – ''Candida glabrata''<br />
+
**[[1a1d]] – yRNAP subunit RPB8 – yeast - NMR<br />
**[[2rf4]] - yRNAP I subunit RPA4<br />
**[[2rf4]] - yRNAP I subunit RPA4<br />
-
**[[1i6h]] - yRNAP II + DNA<br />
+
**[[1nik]], [[nt9]], [[wcm]], [[2b8k]], [[3fki]], [[3qt1]], [[1i3q]], [[1i50]], [[1dzf]] – yRNAP II<br />
-
**[[1nik]], [[1nt9]], [[1wcm]], [[2b8k]], [[3fki]], [[3qt1]], [[1i3q]], [[1i50]], [[1dzf]] – yRNAP II<br />
+
**[[3j1n]], [[4v1n]] – yRNAP II – Cryo EM<br />
-
**[[3j1n]] – yRNAP II – Cryo EM<br />
+
**[[1y14]] - yRNAP II subunits RPB4 RPB7<br />
**[[1y14]] - yRNAP II subunits RPB4 RPB7<br />
-
**[[1pqv]], [[1y1v]], [[4bbr]], [[4bbs]] - yRNAP II + TFIIS<br />
+
 
-
**[[1y1y]] - yRNAP II + TFIIS + DNA +RNA<br />
+
**[[2ckz]]- yRNAP III<br />
-
**[[2vum]] - yRNAP II + inhibitor + DNA + RNA<br />
+
 
-
**[[1r5u]], [[3k7a]], [[3k1f]] - yRNAP II + TFIIB<br />
+
*Eukaryotic DNA-dependent RNAP complex with DNA/RNA
-
**[[1r9s]], [[2ja5]], [[2ja6]], [[2ja7]], [[2ja8]], [[2nvq]], [[2nvt]], [[2nvx]], [[2nvy]], [[2nvz]], [[3gtg]], [[3gtj]], [[3gtk]], [[3gtl]], [[3gtm]], [[3gto]], [[3gtp]], [[3gtq]], [[3hou]], [[3hov]], [[3how]], [[3hox]], [[3hoy]], [[3hoz]], [[3po2]], [[3po3]], [[3m3y]], [[3m4o]], [[3rzd]], [[3rzo]], [[3s14]], [[3s15]], [[3s16]], [[3s17]], [[3s1m]], [[3s1n]], [[3s1q]], [[3s1r]], [[3s2d]], [[3s2h]] - yRNAP II + RNA + DNA<br />
+
 
-
**[[1y1w]], [[1y77]], [[2r7z]], [[2r92]], [[2r93]], [[3h3v]] - yRNAP II + RNA<br />
+
**[[4boc]] – hRNAP + DNA<br />
-
**[[1twa]], [[1twc]], [[1twf]], [[1twg]], [[1twh]] - yRNAP II + nucleotide<br />
+
**[[4lzg]], [[4m04]], [[4m0a]] – hRNAP μ + DNA<br />
 +
**[[1i6h, [[4a3i]] - yRNAP II + DNA<br />
 +
**[[4v1m]] - yRNAP II + DNA – Cryo EM<br />
 +
**[[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<br />
 +
**[[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<br />
**[[2b63]] - yRNAP II + nucleotide + RNA<br />
-
**[[2e2i]], [[2e2j]] - yRNAP II + nucleotide + DNA<br />
+
**[[2e2i]], [[2e2j]]] - yRNAP II + nucleotide + DNA<br />
-
**[[2yu9]], [[3i4m]], [[3i4n]] - yRNAP II + nucleotide + DNA + RNA<br />
+
**[[2yu9, [[3i4m]], [[3i4n]] - yRNAP II + nucleotide + DNA + RNA<br />
-
**[[2ckz]] - yRNAP III<br />
+
**[[2vum]] - yRNAP II + inhibitor + DNA + RNA<br />
-
**[[1ef4]] – MtRNAP subunit RPB10 – ''Methanothermobacter thermautotrophicus''<br />
+
-
**[[1eik]] - MtRNAP subunit RPB5 – NMR<br />
+
-
*Prokaryotic DNA-dependent RNA polymerase
+
*Eukaryotic DNA-dependent RNAP complex with protein
-
**[[1hqm]] – TaRNAP subunits α,β,β’,ω − ''Thermus aquaticus''<br />
+
**[[3o2q]], [[3o2s]] – hRNAP II subunit α C-terminal + symplekin <br />
-
**[[2gho]] - TaRNAP subunits α,β,β’<br />
+
**[[3j0k]] – hRNAP II + TFIIF – Cryo EM <br />
-
**[[1i6v]], [[1ynj]], [[1ynn]] - TaRNAP subunits α,β,β’,ω + antibiotic<br />
+
**[[2lto]] - hRNAP II subunit RPB1 + Tudor domain containing protein 3<br />
-
**[[1l9u]] - TaRNAP subunits α,β,β’,ω + σ factor<br />
+
**[[3spa]] - hRNAP + polypeptide <br />
-
**[[1l9z]] - TaRNAP subunits α,β,β’,ω + σ factor + DNA<br />
+
**[[1pqv]], [[1y1v]], [[4bbr]], [[4bbs]] - yRNAP II + TFIIS<br />
-
**[[2auj]], [[2auk]] - TaRNAP subunit β’ <br />
+
**[[1y1y]] - yRNAP II + TFIIS + DNA +RNA <br />
-
**[[1xpp]] – RNAP subunit L – ''Thermoplasma acidophilum''<br />
+
**[[1r5u]], [[3k7a]], [[3k1f]] - yRNAP II + TFIIB <br />
-
**[[2jzb]] – RNAP subunit α + NUSA transcription elongation factor – ''Yersinia pseudotuberculosis''<br />
+
**[[4v1o]] - yRNAP II + DNA + TIIF + TBP + mediator – Cryo EM<br />
-
**[[2waq]], [[2wb1]], [[4ayb]], [[2y0s]] – SsRNAP - ''Sulfolobus shibata''<br />
+
**[[2l0i]] – yRNAP C-terminal + RTT103 – NMR<br />
-
**[[4b1o]] – SsRNAP + DNA<br />
+
**[[4bxx]], [[4bxz]], [[4by1]], [[4by7]] – yRNAP II + RNA + DNA + transcription factor Bye1<br />
-
**[[3e7h]] – RNAP subunit β – ''Vibrio cholerae''<br />
+
-
*RNA-dependent RNA polymerase
+
*Eukaryotic DNA-dependent RNAP complex with small molecule
-
**[[3phu]], [[1khv]], [[1khw]] – HfRNAP L RNA-directed – Hemorrhagic fever virus<br />
+
**[[3pgl]] - hRNAP II C terminal + inhibitor<br />
-
**[[3phw]], [[2pt2]], [[3pt2]] – HfRNAP + ubiquitin<br />
+
**[[3cqz]], [[1k83]] - yRNAP II + inhibitor<br />
-
**[[3phx]] – HfRNAP + ISG15<br />
+
**[[1twa]], [[1twc]], [[1twf]], [[1twg]], [[1twh]] - yRNAP II + nucleotide<br />
-
**[[3pse]] - HfRNAP + ISG15 (mutant)<br />
+
 
-
**[[2xwh]], [[2xxd]], [[2xhu]], [[2xhw]], [[3i5k]], [[1c2p]], [[1csj]], [[1quv]], [[1yuy]], [[1yv2]], [[1yvx]], [[1yvz]], [[3gsz]], [[4aep]], [[4aex]] – HvRNAP NS5B domain – Hepatitis virus<br />
+
 
 +
RNA-dependent RNAP
 +
 
 +
**[[3phu]], [[1khv]], [[1khw]] – HfRNAP L RNA-directed – Hemorrhagic fever virus<br />
 +
**[[2xwh]], [[2xxd]], [[2xhu]],[[ 2xhw]], [[3i5k]], [[1c2p]], [[1csj]], [[1quv]], [[1yuy]], [[1yv2]], [[1yvx]], [[1yvz]], [[3gsz]], [[4aep]], [[4aex]], [[2wrm]], [[3mwv]], [[3mww]] – HvRNAP Ns5b domain – Hepatitis virus<br />
**[[3vc8]] - HvRNAP cytoplasmic domain C terminal<br />
**[[3vc8]] - HvRNAP cytoplasmic domain C terminal<br />
-
**[[3vcb]] - HvRNAP cytoplasmic domain C terminal (mutant)<br />
+
**[[3vcb]], [[4ry4]], [[4ry5]], [[4ry6]], [[4ry7]] - HvRNAP cytoplasmic domain C terminal (mutant) <br />
-
**[[2xym]], [[2xhv]], [[2xi2]], [[4e76]], [[4adp]] - HvRNAP NS5B domain (mutant)<br />
+
**[[2xym]], [[2xhv]], [[2xi2]], [[4e76]], [[4adp]], [[4obc]], [[4wt9]] - HvRNAP Ns5b domain (mutant) <br />
-
**[[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]] - HvRNAP NS5B domain + inhibitor<br />
+
 
-
**[[3gyn]], [[1os5]], [[3br9]], [[3bsa]], [[3bsc]], [[3cde]], [[3co9]], [[3cwj]], [[3d28]], [[3d5m]], [[3e51]], [[3frz]], [[3igv]], [[3hvo]], [[3h2l]], [[4kai]], [[4kb7]], [[4kbi]], [[4ke5]], [[4khm]], [[4khr]] - HvRNAP NS5B domain (mutant) + inhibitor<br />
+
**[[1rdr]] - PoRNAP – Polio virus<br />
-
**[[2wrm]], [[3mwv]], [[3mww]] – HvRNAP NS5B domain<br />
+
**[[1tql]], [[2ijd]], [[2ijf]], [[4nlo]], [[4nlp]], [[4nlq]], [[4nlr]], [[4nls]], [[4nlt]], [[4nlu]], [[4nlv]], [[4nlw]], [[4nlx]], [[4nly]], [[4r0e]] - PoRNAP (mutant) <br />
-
**[[2xi3]] - HvRNAP NS5B domain (mutant) + nucleotide<br />
+
-
**[[1gx5]], [[1gx6]] - HvRNAP NS5B domain + nucleotide<br />
+
-
**[[4e78]], [[4e7a]] - HvRNAP NS5B domain (mutant) + RNA<br />
+
-
**[[3ol6]], [[2jlg]], [[4k4s]], [[4k4t]], [[4k4u]], [[4k4v]], [[4k4w]] – PoRNAP (mutant) + RNA – Poliovirus<br />
+
-
**[[1rdr]] - PoRNAP <br />
+
-
**[[1tql]], [[2ijd]], [[2ijf]], [[4nlo]], [[4nlp]], [[4nlq]], [[4nlr]], [[4nls]], [[4nlt]], [[4nlu]], [[4nlv]], [[4nlw]], [[4nlx]], [[4nly]] - PoRNAP (mutant)<br />
+
-
**[[3ol7]], [[3ol8]], [[3ol9]], [[3ola]], [[3olb]] - PoRNAP (mutant) + RNA + nucleotide<br />
+
-
**[[2im1]], [[2im0]], [[2im2]], [[2im3]], [[2ily]], [[2ilz]] - PoRNAP (mutant) + nucleotide<br />
+
**[[2xi5]], [[2xi7]] – RNAP L N-terminal – Bunyavirus<br />
**[[2xi5]], [[2xi7]] – RNAP L N-terminal – Bunyavirus<br />
**[[3jsb]] – RNAP (mutant) – Lymphocytic choriomengitis virus<br />
**[[3jsb]] – RNAP (mutant) – Lymphocytic choriomengitis virus<br />
**[[2wk4]], [[2uut]], [[2uuw]] – SvRNAP (mutant) – Sapporo virus<br />
**[[2wk4]], [[2uut]], [[2uuw]] – SvRNAP (mutant) – Sapporo virus<br />
-
**[[2ckw]] - SvRNAP residues 1135-1649<br />
+
**[[2ckw]] - SvRNAP residues 1135-1649 <br />
-
**[[3klv]], [[3kmq]], [[3kms]], [[3kna]], [[3nl0]] – FmRNAP (mutant) + RNA – Foot-and-mouth virus<br />
+
**[[3nky]], [[4wyl]], [[4wyw]] - FmRNAP (mutant) - Foot-and-mouth virus<br />
-
**[[3nky]] - FmRNAP (mutant)<br />
+
**[[1hhs]], [[4a8o]], [[4b02]], [[1hi8]] – P6RNAP – Bacteriophage φ-6<br />
-
**[[3koa]] - FmRNAP (mutant) + RNA + nucleotide<br />
+
**[[2jl9]], [[2jlf]], [[1wac]] – P6RNAP (mutant) <br />
-
**[[1wne]] – FmRNAP + RNA <br />
+
-
**[[2e9r]], [[2e9t]], [[2e9z]], [[2ec0]] - FmRNAP + RNA + inhibitor<br />
+
-
**[[2d7s]], [[2f8e]] – FmRNAP + VPG protein<br />
+
-
**[[1hhs]], [[4a8o]], [[4b02]] – P6RNAP – Bacteriophage φ-6<br />
+
-
**[[2jl9]], [[2jlf]] – P6RNAP (mutant)<br />
+
-
**[[1uvi]], [[1uvl]], [[1uvm]], [[1uvn]], [[4a8f]], [[4a8k]], [[4a8m]], [[4a8q]], [[4a8s]], [[4a8w]], [[4a8y]] – P6RNAP + RNA<br />
+
**[[2po4]] – N4RNAP polymerase domain – Bacteriophage N4<br />
**[[2po4]] – N4RNAP polymerase domain – Bacteriophage N4<br />
-
**[[3c2p]], [[3c3l]], [[3c46]], [[3q0a]] - N4RNAP polymerase domain + promoter DNA<br />
 
**[[1l9k]] – DevRNAP N terminal – Dengue virus<br />
**[[1l9k]] – DevRNAP N terminal – Dengue virus<br />
**[[2j7u]], [[4c11]] - DevRNAP polymerase domain<br />
**[[2j7u]], [[4c11]] - DevRNAP polymerase domain<br />
Line 174: Line 192:
**[[2cjq]] - DvRNAP polymerase domain<br />
**[[2cjq]] - DvRNAP polymerase domain<br />
**[[1sh0]], [[1sh2]], [[1sh3]] - NvRNAP C terminal – Norwalk virus<br />
**[[1sh0]], [[1sh2]], [[1sh3]] - NvRNAP C terminal – Norwalk virus<br />
-
**[[3bsn]], [[3bso]], [[3h5x]], [[3h5y]] - NvRNAP + RNA + nucleotide<br />
 
**[[1vyi]] - RNAP α subunit C terminal – Rabies virus<br />
**[[1vyi]] - RNAP α subunit C terminal – Rabies virus<br />
**[[2hcn]], [[2hcs]], [[2hfz]] – RNAP polymerase domain – West Nile virus<br />
**[[2hcn]], [[2hcs]], [[2hfz]] – RNAP polymerase domain – West Nile virus<br />
**[[2pgg]], [[2pus]] – RNAP – Bursal disease virus<br />
**[[2pgg]], [[2pus]] – RNAP – Bursal disease virus<br />
-
**[[2r7o]], [[2r7q]] – SrRNAP – Simian rotavirus<br />
+
**[[[[2r7o]], [[[[2r7q]] – SrRNAP – Simian rotavirus<br />
-
**[[4f5x]] – SrRNAP + Vp2 + Vp6<br />
+
**[[4au6]] - RNAP – bovine rotavirus – Cryo-EM<br />
**[[4au6]] - RNAP – bovine rotavirus – Cryo-EM<br />
**[[2yi8]], [[2yi9]], [[2yia]], [[2yib]] – IpnvRNAP – Infectious pancreatic necrosis virus<br />
**[[2yi8]], [[2yi9]], [[2yia]], [[2yib]] – IpnvRNAP – Infectious pancreatic necrosis virus<br />
-
**[[3zed]] – IpnvRNAP + capsid protein Vp3<br />
 
**[[3n6l]] – EvRNAP – Human enterovirus<br />
**[[3n6l]] – EvRNAP – Human enterovirus<br />
**[[3n6m]], [[3n6n]] – EvRNAP + nucleotide<br />
**[[3n6m]], [[3n6n]] – EvRNAP + nucleotide<br />
**[[3nah]], [[3nai]], [[3qid]], [[3uqs]] – MnvRNAP – Murine norovirus<br />
**[[3nah]], [[3nai]], [[3qid]], [[3uqs]] – MnvRNAP – Murine norovirus<br />
 +
**[[3ddk]] – CvRNAP RDRP domain – Coxsakievirus<br />
 +
**[[4wfx]], [[4wfy]], [[4wfz]] – CvRNAP RDRP domain (mutant)<br />
 +
**[[2j7n]], [[2j7o]] – RNAP residues 381-1402 – Neurospora crassa<br />
 +
**[[4gzk]], [[4ieg]] – RNAP – cystovirus 12<br />
 +
**[[4i1t]] – RNAP L – Pichinde virus <br />
 +
**[[4miw]] – RNAP L N terminal – Lassa virus <br />
 +
**[[4mtp]] – RNAP RDRP module – Encephalitis virus <br />
 +
**[[4cgx]], [[4chc]] – TvRNAP N terminal – Thogoto virus <br />
 +
**[[4chd]] – TvRNAP 627 domain <br />
 +
**[[4che]], [[4chf]] – TvRNAP cap-binding domain <br />
 +
 +
*RNA-dependent RNAP complex with RNA
 +
 +
**[[4e78]], [[4e7a]], [[4wta]], [[4wtc]], [[4wtd]], [[4wte]], [[4wtf]], [[4wtg]], [[4wti]], [[4wtj]], [[4wtk]], [[4wtl]], [[4wtm]] - HvRNAP Ns5b domain (mutant) + RNA<br />
 +
**[[3ol6]], [[2jlg]], [[4k4s]], [[4k4t]], [[4k4u]], [[4k4v]], [[4k4w]] – PoRNAP (mutant) + RNA <br />
 +
**[[3ol7]], [[3ol8]], [[3ol9]], [[3ola]], [[3olb]] - PoRNAP (mutant) + RNA + nucleotide<br />
 +
**[[3klv]], [[3kmq]], [[3kms]], [[3kna]], [[3nl0]], [[3nma]], [[4iqx]], [[4wzm]] – FmRNAP (mutant) + RNA<br />
 +
**[[3koa]] - FmRNAP (mutant) + RNA + nucleotide<br />
 +
**[[1wne]] – FmRNAP + RNA <br />
 +
**[[2e9r]], [[2e9t]], [[2e9z]], [[2ec0]] - FmRNAP + RNA + inhibitor<br />
 +
**[[1uvi]], [[1uvl]], [[1uvm]], [[1uvn]], [[4a8f]], [[4a8k]], [[4a8m]], [[4a8q]], [[4a8s]], [[4a8w]], [[4a8y – P6RNAP + RNA<br />
 +
**[[3bsn, [[3bso]], [[3h5x]], [[3h5y]] - NvRNAP + RNA + nucleotide<br />
 +
**[[2r7r]], [[2r7s]], [[2r7t]], [[2r7u]], [[2r7v]], [[2r7w]], [[2r7x]] – SrRNAP + RNA<br />
 +
**[[4k50]] – RNAP + RNA – Human rhinovirus<br />
 +
**[[3c2p]], [[3c3l]], [[3c46]], [[3q0a]] - N4RNAP polymerase domain + promoter DNA<br />
 +
**[[1hht]], [[1hi0]] – P6RNAP + DNA<br />
 +
**[[1uvj]], [[1uvk]] – P6RNAP + RNA<br />
 +
**[[4k4x]], [[4k4y]], [[4k4z]] – CvRNAP + RNA<br />
 +
 +
*RNA-dependent RNAP complex with protein
 +
 +
**[[3phw]], [[2pt2]], [[3pt2]] – HfRNAP + ubiquitin<br />
 +
**[[3phx]], [[3pse]] – HfRNAP + ISG15<br />
 +
**[[2d7s]], [[2f8e]] – FmRNAP + VPG protein<br />
 +
**[[3cdw]] - CvRNAP + POP + VPG<br />
 +
**[[4f5x]] – SrRNAP + Vp2 + Vp6<br />
 +
**[[3zed]] – IpnvRNAP + capsid protein Vp3<br />
 +
**[[4hxd]] – RNAP L + polyubiquitin-C – Dugbe virus<br />
 +
 +
*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]] - HvRNAP Ns5b domain + inhibitor<br />
 +
**[[3gyn]], [[1os5]], [[3br9]], [[3bsa]], [[3bsc]], [[3cde]], [[3co9]], [[3cwj]], [[3d28]], [[3d5m]], [[3e51]], [[3frz]], [[3igv]], [[3hvo]], [[3h2l]], [[4kai]], [[4kb7]], [[4kbi]], [[4ke5]], [[4khm]], [[4khr]] - HvRNAP Ns5b domain (mutant) + inhibitor<br />
 +
**[[2xi3]] - HvRNAP Ns5b domain (mutant) + nucleotide<br />
 +
**[[1gx5]], [[1gx6]] - HvRNAP Ns5b domain + nucleotide<br />
 +
**[[2im1]], [[2im0]], [[2im2]], [[2im3]], [[2ily]], [[2ilz]] - PoRNAP (mutant) + nucleotide<br />
**[[3sfg]] – MnvRNAP + thio-uridine<br />
**[[3sfg]] – MnvRNAP + thio-uridine<br />
**[[3sfu]] – MnvRNAP + ribavirine<br />
**[[3sfu]] – MnvRNAP + ribavirine<br />
-
**[[3upf]], [[3ur0]] – MnvRNAP + inhibitor<br />
+
**[[3upf]], [[3ur0]], [[4nru]], [[4o4r]] – MnvRNAP + inhibitor<br />
**[[4lq3]], [[4lq9]] – RNAP + inhibitor – human norovirus <br />
**[[4lq3]], [[4lq9]] – RNAP + inhibitor – human norovirus <br />
-
**[[2r7r]], [[2r7s]], [[2r7t]], [[2r7u]], [[2r7v]], [[2r7w]], [[2r7x]] – SrRNAP + RNA<br />
+
**[[3cdu ]]– CvRNAP + POP<br />
-
**[[3cdu]] – CvRNAP + POP – Coxsakievirus<br />
+
-
**[[3ddk]] - CvRNAP<br />
+
-
**[[3cdw]] - CvRNAP + POP + VPG<br />
+
**[[3eva]], [[3evb]], [[3evc]], [[3evd]], [[3eve]], [[3evf]], [[3evg]] – RNAP N terminal + nucleotide – Yellow fever virus<br />
**[[3eva]], [[3evb]], [[3evc]], [[3evd]], [[3eve]], [[3evf]], [[3evg]] – RNAP N terminal + nucleotide – Yellow fever virus<br />
-
**[[2j7n]], [[2j7o]] – RNAP residues 381-1402 – ''Neurospora crassa''<br />
+
**[[1hi1]] – P6RNAP + nucleotide<br />
-
**[[4hxd]] – RNAP L + polyubiquitin-C – Dugbe virus<br />
+
 
-
**[[4k50]] – RNAP + RNA – Human rhinovirus<br />
+
*Polymerase acidic protein (or PA or subunit P2)
-
**[[4gzk]], [[4ieg]] – RNAP – cystovirus 12<br />
+
 
-
**[[4i1t]] – RNAP L – Pichinde virus <br />
+
**[[3hw3]], [[3hw4]], [[3hw5]] - IvRNAP PA (mutant) + Mn + nucleotide – Influenza virus<br />
-
**[[4miw]] – RNAP L N terminal – Lassa virus <br />
+
**[[3hw6]] - IvRNAP PA (mutant) + Mn<br />
 +
**[[3wi0]] – IvRNAP PA (mutant)<br />
 +
**[[4w9s]] – IvRNAP PA + inhibitor<br />
 +
**[[3cm8]] – IvRNAP PA + RNA-directed RNA polymerase PA peptide<br />
 +
**[[4e5e]] – IvRNAP PA residues 1-50, 73-196 + Mn<br />
 +
**[[4e5f]], [[4e5g]], [[4e5h]], [[4e5i]], [[4e5j]], [[4e5l]] – IvRNAP PA residues 1-50, 73-196 + Mn + inhibitor<br />
 +
**[[3ebj]], [[2w69]] - IvRNAP PA residues 1-256<br />
 +
**[[4iuj]] - IvRNAP PA residues 254-713<br />
 +
 
 +
 
 +
*Polymerase basic protein 2 (or RNAP subunit P3 or PB2)
 +
 
 +
**[[4enf]] – IvRNAP PB2 cap-binding domain<br />
 +
**[[4j2r]] – IvRNAP PB2 middle domain<br />
 +
**[[3cw4]] - IvRNAP PB2 C terminal <br />
 +
**[[2gmo]] - IvRNAP PB2 C terminal - NMR<br />
 +
**[[4eqk]] – IvRNAP PB2 cap-binding domain + nucleotide<br />
 +
**[[4nce]] – IvRNAP PB2 cap-binding domain (mutant) + nucleotide<br />
 +
**[[4ncm]] – IvRNAP PB2 cap-binding domain (mutant) + inhibitor<br />
 +
**[[3wi1]] - IvRNAP PB2 (mutant) + nucleotide<br />
 +
**[[4p1u]] - IvRNAP PB2 + inhibitor<br />
 +
**[[4uad]], [[4uae]], [[4uaf]] - IvRNAP PB2 + importin<br />
 +
**[[2vqz]] - IvRNAP PB2 CAP-binding domain<br />
 +
**[[2vy6]] - IvRNAP PB2 627- and NLS domains<br />
 +
**[[2vy7]] - IvRNAP PB2 627-domain<br />
 +
**[[2vy8]] - IvRNAP PB2 627-domain (mutant) <br />
 +
 
 +
*RNAP PA+PB1
 +
 
 +
**[[2znl]] - IvRNAP PA + PB1<br />
 +
 
 +
*RNAP PB1+PB2
 +
 
 +
**[[2ztt]], [[3a1g]] - IvRNAP PB1 C terminal + RNAP PB2 N terminal<br />
 +
**[[3j9b]] - IvRNAP PB1+PB2 + RNA<br />
 +
 
 +
*RNAP PA+PB1+PB2
-
*Influenza virus RNA polymerase (Polymerase acidic protein - PAP)
+
**[[4wsb]] - IvRNAP PB1 + IvRNAP PA + IvRNAP PB2 + RNA<br />
-
**[[3hw3]], [[3hw4]], [[3hw5]] - IvRNAP subunit P2 (mutant) + Mn + nucleotide – Influenza virus<br />
 
-
**[[3hw6]] - IvRNAP subunit P2 (mutant) + Mn <br />
 
-
**[[3cm8]] - IvPAP subunit P2 + RNA-directed RNA polymerase subunit P2 peptide<br />
 
-
**[[4e5e]] - IvPAP residues 1-50, 73-196 + Mn<br />
 
-
**[[4e5f]], [[4e5g]], [[4e5h]], [[4e5i]], [[4e5j]], [[4e5l]] - IvPAP residues 1-50, 73-196 + Mn + inhibitor<br />
 
-
**[[2znl]] - IvRNAP subunit P1 + PAP subunit P2<br />
 
-
**[[2ztt]], [[3a1g]] - IvRNAP subunit P1 + PAP N terminal<br />
 
-
**[[2w69]] - IvRNAP subunit PA<br />
 
-
**[[4iuj]] - IvRNAP subunit P2<br />
 
-
**[[2gmo]], [[3cw4]] - IvRNAP subunit P3<br />
 
-
**[[2vqz]] - IvRNAP subunit P3 CAP-binding domain<br />
 
-
**[[2vy6]] - IvRNAP subunit P3 627- and NLS domains<br />
 
-
**[[2vy7]] - IvRNAP subunit P3 627-domain<br />
 
-
**[[2vy8]] - IvRNAP subunit P3 627-domain (mutant)<br />
 
*DNA primase
*DNA primase
Line 264: Line 344:
*Poly(A) RNA polymerase
*Poly(A) RNA polymerase
-
**[[3pq1]] – hPAP (mutant)<br />
+
**[[3pq1]] – hRNAP (mutant)<br />
-
**[[4lt6]] – hPAP γ <br />
+
**[[4lt6]] – hRNAP γ <br />
-
**[[4nkt]] – SpPAP (mutant) + UMPNPP <br />
+
**[[4nkt]] – SpRNAP (mutant) + UMPNPP <br />
-
**[[4nku]] – SpPAP (mutant) + RNA <br />
+
**[[4nku]] – SpRNAP (mutant) + RNA <br />
-
**[[3nyb]] – yPAP + AIR2<br />
+
**[[3nyb]] – yRNAP + AIR2<br />
-
**[[4e7x]], [[4e80]], [[4e8f]], [[4ep7]], [[4fh3]] – fyPAP Cid1 – fission yeast<br />
+
**[[4e7x]], [[4e80]], [[4e8f]], [[4ep7]], [[4fh3]] – fyRNAP Cid1 – fission yeast<br />
-
**[[4fh5]], [[4fhp]], [[4fhv]], [[4fhw]], [[4fhy]] – fyPAP Cid1 + nucleotide<br />
+
**[[4fh5]], [[4fhp]], [[4fhv]], [[4fhw]], [[4fhy]] – fyRNAP Cid1 + nucleotide<br />
-
**[[4fhx]] – fyPAP Cid1 (mutant) + nucleotide
+
**[[4ud4]], [[4ud5]] - fyRNAP Cid1 (mutant)<br />
 +
**[[4fhx]] – fyRNAP Cid1 (mutant) + nucleotide
}}
}}
[[Category:Topic Page]]
[[Category:Topic Page]]
*Created with the participation of [[User:Craig T Martin|Craig T Martin]].
*Created with the participation of [[User:Craig T Martin|Craig T Martin]].

Revision as of 11:34, 10 June 2015

Template:STRUCTURE 3m3y

RNA polymerase (RNAP, DNA primase, dnaG) catalyzes the addition of nucleotides to RNA during transcription. DNA primase (DNAP) is RNAP which catalyzes the synthesis of the RNA primer which complements an ssDNA template and initiates DNA synthesis. dnaG is a bacterial primase. Influenza virus RNA polymerase 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. (1qln; blue: nontemplate strand; cyan: template strand; red:RNA). See also Transcription and RNA Processing.
For RNA polymerase from bacteriophage T7 see

For RNA-dependent RNA polymerase from Hepatitis C virus - NS5B - see

For DNA-dependent RNA polymerase see

For the Thermus thermophilus β' subunit see

For the influenza virus RNA-dependent RNA polymerase PB2 and PA homology model and sequence alignment see

3D Structures of RNA polymerase

Updated on 10-June-2015 {{#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 - 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 – RNAP β subunit – Mycobacterium tuberculosis
    • 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 – RNAP 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
  • Prokaryotic DNA-dependent RNAP complex with DNA/RNA
    • 4b1p, 4b1o – SsRNAP + DNA
    • 3q22, 3q23]], 3q24, 4ff1, 4ff2, 4ff3, 4ff4 – RNAP + DNA – Enterobacteria phage N4
    • 2o5i, 2o5j, 4gzy, 4gzz - TtRNAP subunits α,β,β’,ω + DNA +RNA
    • 4wqs - TtRNAP subunits α,β,β’,ω + DNA
    • 2ppb - TtRNAP subunits α,β,β’,ω + antibiotic + DNA + RNA + substrate analog
    • 4igc, 4jk1, 4jk2, 4jkr, 4kmu - EcRNAP subunits α,β,β’,ω + RNA
    • 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
    • 3aoh, 3aoi - TtRNAP subunits α,β,β’,ω + DNA +RNA + GFH1
    • 2be5- TtRNAP subunits α,β,β’,ω + σ factor + inhibitor
    • 2cw0 - 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
    • 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 - TtRNAP subunits α,β,β’,ω + σ factor + DNA
    • 4q5s - TtRNAP subunits α,β,β’,ω + σ factor + DNA + RNA
    • 3dxj, 3eql - TtRNAP subunits α,β,β’,ω + σ factor + antibiotic
    • 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
    • 3t72 - EcRNAP subunit β + Pho box DNA + PhoB
    • 1lb2, 3n4m - EcRNAP subunit α + DNA + CAP
    • 1xs9 - EcRNAP subunit α + DNA + MARA
    • 3n97 - EcRNAP subunit α C terminal + DNA + σ factor
    • 4ljz, 4lk1, 4mey - EcRNAP subunits α,β,β’,ω + RNAP sigma factor
    • 4mex - EcRNAP subunits α,β,β’,ω + RNAP sigma factor + salinamide
    • 4lk0, 4llg - EcRNAP subunits α,β,β’,ω + RNAP sigma factor + RNAP inhibitor
    • 3iyd - EcRNAP subunits α,β,β’,ω + RNAP sigma factor + catabolite gene activator + DNA
    • 4s20 - EcRNAP subunits α,β,β’,ω + RNAP sigma factor + RAPA + DNA
    • 3ihq, 1z3e, 3gfk - BsRNAP subunit α +regulatory protein SPX
    • 1l9u - TaRNAP subunits α,β,β’,ω + σ factor
    • l9z - TaRNAP subunits α,β,β’,ω + σ factor + DNA
    • 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 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

    • 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
    • 2xub, 2xv4 - hRNAP III subunits RPC3
    • 2dk8 – RNAP III RPC34 domain - mouse – NMR
    • 2dk5 – hRNAP III winged helix domain (mutant) – NMR
    • 2yu3 - hRNAP III winged helix domain
  • Eukaryotic DNA-dependent RNAP complex with DNA/RNA
  • Eukaryotic DNA-dependent RNAP complex with protein
    • 3o2q, 3o2s – hRNAP II subunit α C-terminal + symplekin
    • 3j0k – hRNAP II + TFIIF – Cryo EM
    • 2lto - hRNAP II subunit RPB1 + Tudor domain containing protein 3
    • 3spa - hRNAP + polypeptide
    • 1pqv, 1y1v, 4bbr, 4bbs - yRNAP II + TFIIS
    • 1y1y - yRNAP II + TFIIS + DNA +RNA
    • 1r5u, 3k7a, 3k1f - yRNAP II + TFIIB
    • 4v1o - 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
  • Eukaryotic DNA-dependent RNAP complex with small molecule


RNA-dependent RNAP

    • 1rdr - PoRNAP – Polio virus
    • 1tql, 2ijd, 2ijf, 4nlo, 4nlp, 4nlq, 4nlr, 4nls, 4nlt, 4nlu, 4nlv, 4nlw, 4nlx, 4nly, 4r0e - PoRNAP (mutant)
    • 2xi5, 2xi7 – RNAP 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 - FmRNAP (mutant) - Foot-and-mouth virus
    • 1hhs, 4a8o, 4b02, 1hi8 – P6RNAP – Bacteriophage φ-6
    • 2jl9, 2jlf, 1wac – P6RNAP (mutant)
    • 2po4 – N4RNAP polymerase domain – Bacteriophage N4
    • 1l9k – DevRNAP N terminal – Dengue virus
    • 2j7u, 4c11 - DevRNAP polymerase domain
    • 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
    • 3n6m, 3n6n – EvRNAP + nucleotide
    • 3nah, 3nai, 3qid, 3uqs – MnvRNAP – Murine norovirus
    • 3ddk – CvRNAP RDRP domain – Coxsakievirus
    • 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
    • 4miw – 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
  • RNA-dependent RNAP complex with RNA
  • RNA-dependent RNAP complex with protein
    • 3phw, 2pt2, 3pt2 – HfRNAP + ubiquitin
    • 3phx, 3pse – HfRNAP + ISG15
    • 2d7s, 2f8e – FmRNAP + VPG protein
    • 3cdw - CvRNAP + POP + VPG
    • 4f5x – SrRNAP + Vp2 + Vp6
    • 3zed – IpnvRNAP + capsid protein Vp3
    • 4hxd – RNAP L + polyubiquitin-C – Dugbe virus
  • RNA-dependent RNAP complex with small molecule
  • Polymerase acidic protein (or PA or subunit P2)
    • 3hw3, 3hw4, 3hw5 - IvRNAP PA (mutant) + Mn + nucleotide – Influenza virus
    • 3hw6 - IvRNAP PA (mutant) + Mn
    • 3wi0 – IvRNAP PA (mutant)
    • 4w9s – IvRNAP PA + inhibitor
    • 3cm8 – IvRNAP PA + RNA-directed RNA polymerase PA peptide
    • 4e5e – IvRNAP PA residues 1-50, 73-196 + Mn
    • 4e5f, 4e5g, 4e5h, 4e5i, 4e5j, 4e5l – IvRNAP PA residues 1-50, 73-196 + Mn + inhibitor
    • 3ebj, 2w69 - IvRNAP PA residues 1-256
    • 4iuj - IvRNAP PA residues 254-713


  • Polymerase basic protein 2 (or RNAP subunit P3 or PB2)
    • 4enf – IvRNAP PB2 cap-binding domain
    • 4j2r – IvRNAP PB2 middle domain
    • 3cw4 - IvRNAP PB2 C terminal
    • 2gmo - IvRNAP PB2 C terminal - NMR
    • 4eqk – IvRNAP PB2 cap-binding domain + nucleotide
    • 4nce – IvRNAP PB2 cap-binding domain (mutant) + nucleotide
    • 4ncm – IvRNAP PB2 cap-binding domain (mutant) + inhibitor
    • 3wi1 - IvRNAP PB2 (mutant) + nucleotide
    • 4p1u - IvRNAP PB2 + inhibitor
    • 4uad, 4uae, 4uaf - IvRNAP PB2 + importin
    • 2vqz - IvRNAP PB2 CAP-binding domain
    • 2vy6 - IvRNAP PB2 627- and NLS domains
    • 2vy7 - IvRNAP PB2 627-domain
    • 2vy8 - IvRNAP PB2 627-domain (mutant)
  • RNAP PA+PB1
    • 2znl - IvRNAP PA + PB1
  • RNAP PB1+PB2
    • 2ztt, 3a1g - IvRNAP PB1 C terminal + RNAP PB2 N terminal
    • 3j9b - IvRNAP PB1+PB2 + RNA
  • RNAP PA+PB1+PB2
    • 4wsb - IvRNAP PB1 + IvRNAP PA + IvRNAP PB2 + RNA


  • DNA primase
    • 4lik - hDNAP small subunit
    • 4lil - hDNAP small subunit + UTP
    • 3q36 – hDNAP large subunit
    • 4bpu - hDNAP small (mutant) + large subunit
    • 4bpw - hDNAP small (mutant) + large subunit + UTP
    • 4bpx - hDNAP small (mutant) + DNA polymerase α subunit
    • 4ehs – HpDNAP C terminal
    • 4lim - yDNAP small subunit
    • 3lgb - yDNAP large subunit
    • 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
    • 1v34 - PhDNAP small subunit + nucleotide
    • 1g71 - PfDNAP small subunit
    • 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
    • 4e2k – SaDNAP – Staphylococcus aureus
    • 2lzn – SaDNAP C terminal – NMR
    • 4edg, 4edk, 4edr, 4edt, 4edv, 4ee1 – SaDNAP + nucleotide
  • Bacterial primase
    • 2r6a, 2r6c - GsdnaG helicase binding domain + helicase – Geobacillus stearothermophilus
    • 4m4w - GsdnaG helicase binding domain + helicase + DnaI
    • 1d0q - GsDNAP zinc-binding domain
    • 1z8s - GsdnaG dnaB binding domain - NMR
    • 2haj - EcdnaG catalytic domain - NMR
    • 3b39 – EcdnaG catalytic domain + DNA
    • 1t3w – EcdnaG C-terminal
    • 1eqn, 1dd9, 1dde – EcdnaG catalytic core
  • RNA polymerase from Bacteriophage T7
  • Poly(A) RNA polymerase

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

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