RNA polymerase

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Line 178: Line 178:
**[[3h0g]] – fyRNAP II<br />
**[[3h0g]] – fyRNAP II<br />
**[[5u0s]] – fyRNAP II + mediator complex – Cryo EM<br />
**[[5u0s]] – fyRNAP II + mediator complex – Cryo EM<br />
- 
-
*Eukaryotic DNA-dependent RNAP III
 
- 
-
**[[2xub]], [[2xv4]] - hRNAP III subunits RPC3<br />
 
-
**[[5afq]] - hRNAP III subunits RPC3 + RPC32B<br />
 
-
**[[2dk8]] – RNAP III RPC34 domain - mouse – NMR<br />
 
-
**[[2dk5]] – hRNAP III winged helix domain (mutant) – NMR<br />
 
-
**[[2yu3]] - hRNAP III winged helix domain<br />
 
-
**[[2ckz]], [[5fj9]], [[5fja]], [[6eu3]], [[6eu2]] - yRNAP III - Cryo EM<br />
 
-
**[[5fj8]], [[6f41]] - yRNAP III + DNA + RNA - Cryo EM<br />
 
-
**[[6f44]], [[6f42]], [[6f40]], [[6eu1]] - yRNAP III + DNA – Cryo EM<br />
 
-
**[[6cnf]], [[6cnd]], [[6cnc]], [[6cnb]] - yRNAP III + DNA + TFIIIB – Cryo EM<br />
 
-
**[[5xon]] - yRNAP III + DNA + RNA + TFIIB + SPT4 + SPT5 – Cryo EM<br />
 
-
**[[5xog]] - yRNAP III + DNA + RNA + SPT5 + KOW5 + ELF1 – Cryo EM<br />
 
-
**[[6eu0]] - yRNAP III + DNA + TFIIIB + TATA-box-binding protein – Cryo EM<br />
 
-
**[[3ayh]] - fyRNAP III subunit Rpc8+Rpc9<br />
 
- 
-
*Eukaryotic DNA-dependent RNAP μ
 
- 
-
**[[4lzd]] – hRNAP μ<br />
 
-
**[[4lzg]], [[4m04]], [[4m0a]], [[5twp]], [[5twq]], [[5twr]], [[5tws]]. [[5txx]], [[5txz]], [[5tyb]], [[5tyc]], [[5tyd]], [[5tye]], [[5tyf]], [[5tyg]], [[5tyu]], [[5tyv]], [[5tyw]], [[5tyx]], [[5tyy]], [[5tyz]] – hRNAP μ + DNA<br />
 
-
**[[5vzi]], [[5vzh]], [[5vzg]], [[5vzf]], [[5vze]], [[5vzd]], [[5vzc]], [[5vzb]], [[5vza]], [[5vz9]], [[5vz8]], [[5vz7]] – hRNAP μ (mutant) + DNA + nucleotide<br />
 
- 
-
*Eukaryotic DNA-dependent RNAP mitochondrial
 
- 
-
**[[4boc]] – hRNAP + DNA<br />
 
-
**[[6erq]], [[6erp]] – hRNAP + DNA + MTTFA + dimethyladenosine transferase<br />
 
-
**[[3spa]] - hRNAP + polypeptide <br />
 
*''Eukaryotic DNA-dependent RNAP II complex with DNA/RNA''
*''Eukaryotic DNA-dependent RNAP II complex with DNA/RNA''
Line 236: Line 208:
**[[6exv]] – pRNAP II + RNA + DNA + amatoxin – Cryo EM<br />
**[[6exv]] – pRNAP II + RNA + DNA + amatoxin – Cryo EM<br />
-
*''Eukaryotic DNA-dependent RNAP complex with small molecule''
+
*''Eukaryotic DNA-dependent RNAP II complex with small molecule''
**[[3pgl]] - hRNAP II C terminal + inhibitor<br />
**[[3pgl]] - hRNAP II C terminal + inhibitor<br />
**[[3cqz]], [[1k83]] - yRNAP II + inhibitor<br />
**[[3cqz]], [[1k83]] - yRNAP II + inhibitor<br />
**[[1twa]], [[1twc]], [[1twf]], [[1twg]], [[1twh]] - yRNAP II + nucleotide<br />
**[[1twa]], [[1twc]], [[1twf]], [[1twg]], [[1twh]] - yRNAP II + nucleotide<br />
 +
 +
*Eukaryotic DNA-dependent RNAP III
 +
 +
**[[2xub]], [[2xv4]] - hRNAP III subunits RPC3<br />
 +
**[[5afq]] - hRNAP III subunits RPC3 + RPC32B<br />
 +
**[[2dk8]] – RNAP III RPC34 domain - mouse – NMR<br />
 +
**[[2dk5]] – hRNAP III winged helix domain (mutant) – NMR<br />
 +
**[[2yu3]] - hRNAP III winged helix domain<br />
 +
**[[2ckz]], [[5fj9]], [[5fja]], [[6eu3]], [[6eu2]] - yRNAP III - Cryo EM<br />
 +
**[[5fj8]], [[6f41]] - yRNAP III + DNA + RNA - Cryo EM<br />
 +
**[[6f44]], [[6f42]], [[6f40]], [[6eu1]] - yRNAP III + DNA – Cryo EM<br />
 +
**[[6cnf]], [[6cnd]], [[6cnc]], [[6cnb]] - yRNAP III + DNA + TFIIIB – Cryo EM<br />
 +
**[[5xon]] - yRNAP III + DNA + RNA + TFIIB + SPT4 + SPT5 – Cryo EM<br />
 +
**[[5xog]] - yRNAP III + DNA + RNA + SPT5 + KOW5 + ELF1 – Cryo EM<br />
 +
**[[6eu0]] - yRNAP III + DNA + TFIIIB + TATA-box-binding protein – Cryo EM<br />
 +
**[[3ayh]] - fyRNAP III subunit Rpc8+Rpc9<br />
 +
 +
*Eukaryotic DNA-dependent RNAP μ
 +
 +
**[[4lzd]] – hRNAP μ<br />
 +
**[[4lzg]], [[4m04]], [[4m0a]], [[5twp]], [[5twq]], [[5twr]], [[5tws]]. [[5txx]], [[5txz]], [[5tyb]], [[5tyc]], [[5tyd]], [[5tye]], [[5tyf]], [[5tyg]], [[5tyu]], [[5tyv]], [[5tyw]], [[5tyx]], [[5tyy]], [[5tyz]] – hRNAP μ + DNA<br />
 +
**[[5vzi]], [[5vzh]], [[5vzg]], [[5vzf]], [[5vze]], [[5vzd]], [[5vzc]], [[5vzb]], [[5vza]], [[5vz9]], [[5vz8]], [[5vz7]] – hRNAP μ (mutant) + DNA + nucleotide<br />
 +
 +
*Eukaryotic DNA-dependent RNAP mitochondrial
 +
 +
**[[4boc]] – hRNAP + DNA<br />
 +
**[[6erq]], [[6erp]] – hRNAP + DNA + MTTFA + dimethyladenosine transferase<br />
 +
**[[3spa]] - hRNAP + polypeptide <br />
 +
 +
*''DNA primase''
*''DNA primase''
Line 247: Line 249:
**[[4lil]] - hDNAP small subunit + UTP<br />
**[[4lil]] - hDNAP small subunit + UTP<br />
**[[3q36]] – hDNAP large subunit<br />
**[[3q36]] – hDNAP large subunit<br />
 +
**[[5i7m]] – hDNAP large subunit (mutant)<br />
**[[4bpu]] - hDNAP small (mutant) + large subunit<br />
**[[4bpu]] - hDNAP small (mutant) + large subunit<br />
**[[4bpw]] - hDNAP small (mutant) + large subunit + UTP<br />
**[[4bpw]] - hDNAP small (mutant) + large subunit + UTP<br />
Line 253: Line 256:
**[[4lim]] - yDNAP small subunit<br />
**[[4lim]] - yDNAP small subunit<br />
**[[3lgb]] - yDNAP large subunit<br />
**[[3lgb]] - yDNAP large subunit<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 />
 
-
**[[4edg]], [[4edk]], [[4edr]], [[4edt]], [[4edv]], [[4ee1]] – SaDNAP + nucleotide
 
*''Bacterial primase''
*''Bacterial primase''
Line 273: Line 267:
**[[1t3w]] – EcdnaG C-terminal<br />
**[[1t3w]] – EcdnaG C-terminal<br />
**[[1eqn]], [[1dd9]], [[1dde]] – EcdnaG catalytic core<br />
**[[1eqn]], [[1dd9]], [[1dde]] – EcdnaG catalytic core<br />
 +
**[[5w33]] - MtudnaG <br />
 +
**[[5w36]], [[5w35]], [[5w34]] - MtudnaG + DNA<br />
 +
**[[5vaz]] – dnaG – ''Pseudomonas aeruginosa'' <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 />
 +
**[[4edg]], [[4edk]], [[4edr]], [[4edt]], [[4edv]], [[4ee1]] – SaDNAP + nucleotide
 +
*''RNA polymerase from Bacteriophage T7''
*''RNA polymerase from Bacteriophage T7''

Revision as of 06:49, 21 October 2018

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

3D Structures of RNA polymerase

Updated on 21-October-2018




References

  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:http://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:http://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:http://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:http://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:http://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:http://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

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