RNA polymerase
From Proteopedia
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<StructureSection load='3m3y' size='350' side='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) (PDB code [[3m3y]]).' scene='RNA_polymerase/Cv/1'> | <StructureSection load='3m3y' size='350' side='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) (PDB code [[3m3y]]).' scene='RNA_polymerase/Cv/1'> | ||
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**[[3cdw]] - CvRNAP + POP + VPG<br /> | **[[3cdw]] - CvRNAP + POP + VPG<br /> | ||
**[[4f5x]] – SrRNAP + Vp2 + Vp6<br /> | **[[4f5x]] – SrRNAP + Vp2 + Vp6<br /> | ||
| + | **[[5h0r]] – RNAP + Vp4 + RNA - BMCPV<br /> | ||
**[[3zed]] – IpnvRNAP + capsid protein Vp3<br /> | **[[3zed]] – IpnvRNAP + capsid protein Vp3<br /> | ||
**[[4hxd]] – RNAP L + polyubiquitin-C – Dugbe virus<br /> | **[[4hxd]] – RNAP L + polyubiquitin-C – Dugbe virus<br /> | ||
| + | **[[4r71]] – RNAP b chain + EF-TS EF-TU + RPS1 – Enterobacteria phage qbeta<br /> | ||
| + | **[[5jze]] – RNAP + ISG15 – Erve virus<br /> | ||
*''RNA-dependent RNAP complex with small molecule'' | *''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 /> | + | **[[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<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 /> | + | **[[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<br /> |
**[[2xi3]] - HvRNAP Ns5b domain (mutant) + nucleotide<br /> | **[[2xi3]] - HvRNAP Ns5b domain (mutant) + nucleotide<br /> | ||
**[[1gx5]], [[1gx6]] - HvRNAP Ns5b domain + nucleotide<br /> | **[[1gx5]], [[1gx6]] - HvRNAP Ns5b domain + nucleotide<br /> | ||
**[[2im1]], [[2im0]], [[2im2]], [[2im3]], [[2ily]], [[2ilz]] - PoRNAP (mutant) + nucleotide<br /> | **[[2im1]], [[2im0]], [[2im2]], [[2im3]], [[2ily]], [[2ilz]] - PoRNAP (mutant) + nucleotide<br /> | ||
| + | **[[3n6m]], [[3n6n]] – EvRNAP + nucleotide<br /> | ||
**[[3sfg]] – MnvRNAP + thio-uridine<br /> | **[[3sfg]] – MnvRNAP + thio-uridine<br /> | ||
**[[3sfu]] – MnvRNAP + ribavirine<br /> | **[[3sfu]] – MnvRNAP + ribavirine<br /> | ||
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**[[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 /> | ||
**[[1hi1]] – P6RNAP + nucleotide<br /> | **[[1hi1]] – P6RNAP + nucleotide<br /> | ||
| + | **[[5cx6]], [[5cyr]] - TavRNAP + nucleotide<br /> | ||
| + | **[[5hmw]], [[5f3t]], [[5hmx]], [[5hmy]], [[5hn0]], [[5hmz]], [[5iq6]], [[5k5m]] - DevRNAP Ns5 + inhibitor<br /> | ||
| + | **[[5ehg]] - DevRNAP NS5 + SAM + inhibitor<br /> | ||
| + | **[[5goz]], [[5gp1]] - ZvRNAP NS5 + SAH + GTP <br /> | ||
| + | **[[5ltn]], [[5t2t]] - LcmvRNAP + inhibitor<br /> | ||
| - | * | + | *Influenza virus polymerase acidic protein (or PA or subunit P2) |
**[[3hw3]], [[3hw4]], [[3hw5]] - IvRNAP PA (mutant) + Mn + nucleotide – Influenza virus<br /> | **[[3hw3]], [[3hw4]], [[3hw5]] - IvRNAP PA (mutant) + Mn + nucleotide – Influenza virus<br /> | ||
**[[3hw6]] - IvRNAP PA (mutant) + Mn<br /> | **[[3hw6]] - IvRNAP PA (mutant) + Mn<br /> | ||
**[[3wi0]] – IvRNAP PA (mutant)<br /> | **[[3wi0]] – IvRNAP PA (mutant)<br /> | ||
| - | **[[4w9s]] – IvRNAP PA + inhibitor<br /> | + | **[[4w9s]], [[5fdd]], [[5fdg]], [[5i13]], [[5ieq]], [[5if2]], [[5if5]], [[5if7]], [[5if8]], [[5ifb]], [[5ifc]], [[5ifd]] – IvRNAP PA + inhibitor<br /> |
**[[3cm8]] – IvRNAP PA + RNA-directed RNA polymerase PA peptide<br /> | **[[3cm8]] – IvRNAP PA + RNA-directed RNA polymerase PA peptide<br /> | ||
| - | **[[4e5e]] – IvRNAP PA residues 1-50, 73-196 + Mn<br /> | + | **[[4wrt]], [[4wsa]] – IvRNAP PA + PB2 + RNA-directed RNA polymerase PA + RNA<br /> |
| - | **[[4e5f]], [[4e5g]], [[4e5h]], [[4e5i]], [[4e5j]], [[4e5l]] – IvRNAP PA residues 1-50, 73-196 + Mn + inhibitor<br /> | + | **[[4e5e]], [[4zqq]], [[5jht]], [[5jhv]] – IvRNAP PA residues 1-50, 73-196 + Mn<br /> |
| + | **[[4e5f]], [[4e5g]], [[4e5h]], [[4e5i]], [[4e5j]], [[4e5l]], [[4yyl]], [[4zhz]], [[4zi0]] – IvRNAP PA residues 1-50, 73-196 + Mn + inhibitor<br /> | ||
**[[3ebj]], [[2w69]] - IvRNAP PA residues 1-256<br /> | **[[3ebj]], [[2w69]] - IvRNAP PA residues 1-256<br /> | ||
**[[4iuj]] - IvRNAP PA residues 254-713<br /> | **[[4iuj]] - IvRNAP PA residues 254-713<br /> | ||
| - | * | + | *Influenza virus polymerase basic protein 2 (or RNAP subunit P3 or PB2) |
| - | **[[4enf]] – IvRNAP PB2 cap-binding domain<br /> | + | **[[4enf]], [[4u6o]], [[4j2r]], [[2vqz]], [[5ef9]], [[5eg9]] – IvRNAP PB2 cap-binding domain<br /> |
**[[4j2r]] – IvRNAP PB2 middle domain<br /> | **[[4j2r]] – IvRNAP PB2 middle domain<br /> | ||
**[[3cw4]] - IvRNAP PB2 C terminal <br /> | **[[3cw4]] - IvRNAP PB2 C terminal <br /> | ||
**[[2gmo]] - IvRNAP PB2 C terminal - NMR<br /> | **[[2gmo]] - IvRNAP PB2 C terminal - NMR<br /> | ||
| - | **[[4eqk]] – IvRNAP PB2 cap-binding domain + nucleotide<br /> | + | **[[4eqk]], [[5efa]], [[5efc]] – IvRNAP PB2 cap-binding domain + nucleotide<br /> |
| - | **[[4nce]] – IvRNAP PB2 cap-binding domain (mutant) + nucleotide<br /> | + | **[[4nce]], [[3wi1]] – IvRNAP PB2 cap-binding domain (mutant) + nucleotide<br /> |
**[[4ncm]] – IvRNAP PB2 cap-binding domain (mutant) + inhibitor<br /> | **[[4ncm]] – IvRNAP PB2 cap-binding domain (mutant) + inhibitor<br /> | ||
| - | **[[ | + | **[[4p1u]], [[4yd0]], [[5buh]], [[5jun]], [[5jur]] - IvRNAP PB2 cap-binding domain + inhibitor<br /> |
| - | + | ||
**[[4uad]], [[4uae]], [[4uaf]] - IvRNAP PB2 + importin<br /> | **[[4uad]], [[4uae]], [[4uaf]] - IvRNAP PB2 + importin<br /> | ||
| - | **[[2vqz]] - IvRNAP PB2 CAP-binding domain<br /> | ||
**[[2vy6]] - IvRNAP PB2 627- and NLS domains<br /> | **[[2vy6]] - IvRNAP PB2 627- and NLS domains<br /> | ||
**[[2vy7]] - IvRNAP PB2 627-domain<br /> | **[[2vy7]] - IvRNAP PB2 627-domain<br /> | ||
**[[2vy8]] - IvRNAP PB2 627-domain (mutant) <br /> | **[[2vy8]] - IvRNAP PB2 627-domain (mutant) <br /> | ||
| - | *RNAP PA+PB1 | + | *Influenza virus RNAP PA+PB1 |
**[[2znl]] - IvRNAP PA + PB1<br /> | **[[2znl]] - IvRNAP PA + PB1<br /> | ||
| - | *RNAP PB1+PB2 | + | *Influenza virus RNAP PB1+PB2 |
**[[2ztt]], [[3a1g]] - IvRNAP PB1 C terminal + RNAP PB2 N terminal<br /> | **[[2ztt]], [[3a1g]] - IvRNAP PB1 C terminal + RNAP PB2 N terminal<br /> | ||
**[[3j9b]] - IvRNAP PB1+PB2 + RNA<br /> | **[[3j9b]] - IvRNAP PB1+PB2 + RNA<br /> | ||
| - | * | + | *Influenza virus pRNAP PA+PB1+PB2 |
| - | **[[4wsb]] - IvRNAP PB1 + IvRNAP PA + IvRNAP PB2 + RNA<br /> | + | **[[4wsb]], [[5fmz]], [[5m3h]], [[5m3j]], [[5msg]] - IvRNAP PB1 + IvRNAP PA + IvRNAP PB2 + RNA<br /> |
| + | **[[5d98]], [[5d9a]] - IvRNAP PB1 + IvRNAP PA + IvRNAP PB2<br /> | ||
*Poly(A) RNA polymerase | *Poly(A) RNA polymerase | ||
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**[[4nku]] – SpRNAP (mutant) + RNA <br /> | **[[4nku]] – SpRNAP (mutant) + RNA <br /> | ||
**[[3nyb]] – yRNAP + AIR2<br /> | **[[3nyb]] – yRNAP + AIR2<br /> | ||
| - | **[[4e7x]], [[4e80]], [[4e8f]], [[4ep7]], [[4fh3]] – fyRNAP Cid1 | + | **[[4e7x]], [[4e80]], [[4e8f]], [[4ep7]], [[4fh3]] – fyRNAP Cid1 <br /> |
**[[4fh5]], [[4fhp]], [[4fhv]], [[4fhw]], [[4fhy]] – fyRNAP Cid1 + nucleotide<br /> | **[[4fh5]], [[4fhp]], [[4fhv]], [[4fhw]], [[4fhy]] – fyRNAP Cid1 + nucleotide<br /> | ||
**[[4ud4]], [[4ud5]] - fyRNAP Cid1 (mutant)<br /> | **[[4ud4]], [[4ud5]] - fyRNAP Cid1 (mutant)<br /> | ||
| - | **[[4fhx]] – fyRNAP Cid1 (mutant) + nucleotide | + | **[[4fhx]] – fyRNAP Cid1 (mutant) + nucleotide<br /> |
| + | **[[4zrl]] – CeRNAP gld-2 + germline development defective 3 – ''Caenorhabidis elegans'' <br /> | ||
| + | **[[5jnb]] – CeRNAP gld-2 (mutant) + RNP-8 <br /> | ||
| + | |||
}} | }} | ||
== References == | == References == | ||
Revision as of 11:06, 31 October 2017
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3D Structures of RNA polymerase
Updated on 31-October-2017
`**5lts - LcmvRNAP (mutant)
References
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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:http://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:http://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:http://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
- Created with the participation of Craig T Martin.
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