MolNFT v2 · #211491 · protein + DNA + RNA
RNA polymerase II transcribing a chromatosome (type II)
8H0W · DNA-directed RNA polymerase subunit: “RNA polymerase II transcribing a chromatosome (type II)”. Electron microscopy at 4.6, 2 ligands (ZN, MG), 20 pockets (best druggability 0.87). MolNFT v2 #211491 on GenesisL1: 3D structure…
- PDB
- 8H0W
- Type
- protein + DNA + RNA
- Length
- 5,181 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.6
- Source
- Homo sapiens; Komagataella phaffii; SYNTHETIC CONSTRUCT
- Molecule
- DNA-directed RNA polymerase subunit; DNA-directed RNA polymerase subunit beta; RNA…
- EC
- 2.7.7.6
- UniProt
- C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, P68431, P62805, P04908, P06899, P16403
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 4.6 · 23 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit (EC 2.7.7.6) | protein | 1412 | 41% helix, 16% strand | C4R4Y0 |
| B | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1161 | 28% helix, 26% strand | C4QZQ7 |
| C | RNA polymerase II third largest subunit B44, part of central core | protein | 263 | 22% helix, 31% strand | C4R7L2 |
| D | RNA polymerase II subunit B32 | protein | 168 | 53% helix, 6% strand | C4R2U9 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 213 | 39% helix, 25% strand | C4R3P8 |
| F | RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III | protein | 84 | 31% helix, 17% strand | C4R1V1 |
| G | RNA polymerase II subunit | protein | 171 | 13% helix, 44% strand | C4R9A1 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 133 | 8% helix, 48% strand | C4R273 |
| I | DNA-directed RNA polymerase subunit | protein | 111 | 5% helix, 28% strand | F2QPE6 |
| J | RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III | protein | 66 | 42% helix, 5% strand | C4R009 |
| K | RNA polymerase II subunit B12.5 | protein | 113 | 36% helix, 24% strand | C4R3Z5 |
| L | RNA polymerase subunit ABC10-alpha | protein | 45 | 0% helix, 33% strand | F2QMI1 |
| P | RNA (5'-R(P*CP*AP*AP*UP*AP*GP*GP*AP*GP*CP*UP*UP*AP*C)-3') | rna | 14 | — | — |
| T | DNA (261-mer) | dna | 205 | — | — |
| N | DNA (261-mer) | dna | 196 | — | — |
| a | Histone H3.1 | protein | 97 | 65% helix, 4% strand | P68431 |
| b | Histone H4 | protein | 83 | 59% helix, 7% strand | P62805 |
| c, g | Histone H2A type 1-B/E | protein | 105 | 52% helix, 6% strand | P04908 |
| d | Histone H2B type 1-J | protein | 95 | 74% helix, 4% strand | P06899 |
| e | Histone H3.1 | protein | 97 | 66% helix, 4% strand | P68431 |
| f | Histone H4 | protein | 78 | 63% helix, 8% strand | P62805 |
| h | Histone H2B type 1-J | protein | 93 | 75% helix, 4% strand | P06899 |
| u | Histone H1.2 | protein | 73 | 51% helix, 15% strand | P16403 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.87 | 0.89 | 140 | empty |
| 2 | 1175 | 0.86 | 0.87 | 123 | empty |
| 3 | 835 | 0.83 | 0.85 | 112 | empty |
| 4 | 1119 | 0.82 | 0.83 | 100 | empty |
| 5 | 354 | 0.81 | 0.91 | 46 | empty |
Interfaces
77 interfaces between chains.
- A–B · 9620 Ų buried · 113 hydrogen bonds · protein-protein
- T–N · 8657 Ų buried · 691 hydrogen bonds · nucleic-nucleic
- c–d · 2630 Ų buried · 23 hydrogen bonds · protein-protein
- a–b · 2588 Ų buried · 24 hydrogen bonds · protein-protein
- g–h · 2562 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- P68431 · AlphaFold monomer V2.0 prediction for histone H3.1 (P68431) · a predicted model of the same protein · chain a against A, TM-score 0.99
- P06899 · AlphaFold monomer V2.0 prediction for histone H2B type 1-J (P06899) · a predicted model of the same protein · chain h against A, TM-score 0.98
- P62805 · AlphaFold monomer V2.0 prediction for histone H4 (P62805) · a predicted model of the same protein · chain f against A, TM-score 0.98
- P04908 · AlphaFold monomer V2.0 prediction for histone H2A type 1-B/E (P04908) · a predicted model of the same protein · chain g against A, TM-score 0.96
- P16403 · AlphaFold monomer V2.0 prediction for histone H1.2 (P16403) · a predicted model of the same protein · chain u against A, TM-score 0.95
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt C4R4Y0
- Every structure of UniProt C4QZQ7
- Every structure of UniProt C4R7L2
- Every structure of UniProt C4R2U9
- Every structure of UniProt C4R3P8
- Every structure of UniProt C4R1V1
- Every structure of UniProt C4R9A1
- Every structure of UniProt C4R273
- Every structure of UniProt F2QPE6
- Every structure of UniProt C4R009
- Every structure of UniProt C4R3Z5
- Every structure of UniProt F2QMI1
- Every structure of UniProt P68431
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt P06899
- Every structure of UniProt P16403
- Elsewhere: RCSB PDB 8H0W · PDBe 8H0W · UniProt C4R4Y0 · UniProt C4QZQ7 · UniProt C4R7L2 · UniProt C4R2U9 · UniProt C4R3P8 · UniProt C4R1V1 · UniProt C4R9A1 · UniProt C4R273 · UniProt F2QPE6 · UniProt C4R009 · UniProt C4R3Z5 · UniProt F2QMI1 · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt P16403
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