Research workbench
RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W)
Analyse RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8BZ1
- Type
- protein + DNA
- Length
- 6,063 residues
- Chains
- 28
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.8
- Source
- Homo sapiens; Sus scrofa; Xenopus laevis; SYNTHETIC CONSTRUCT
- Molecule
- DNA-directed RNA polymerase subunit; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6, 2.3.1.48, 3.6.4.12
- UniProt
- A0A8D1DPV6, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, F1SKN8, I3LJZ9, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, I3LN51, Q00403, P20226, P35269, P13984, P52655, P52657, P84233, P62799, P06897, P02281
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · resolution 3.8 · 27 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit (EC 2.7.7.6) | protein | 1423 | 43% helix, 16% strand | A0A8D1DPV6 |
| B | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1136 | 31% helix, 25% strand | I3LGP4 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 257 | 26% helix, 29% strand | I3LCH3 |
| D | RNA polymerase II subunit D | protein | 128 | 61% helix, 4% strand | A0A287ADR4 |
| E | DNA-directed RNA polymerase II subunit E | protein | 209 | 39% helix, 22% strand | I3LSI7 |
| F | DNA-directed RNA polymerase II subunit F | protein | 89 | 36% helix, 15% strand | F1SKN8 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 11% helix, 54% strand | I3LJZ9 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 148 | 5% helix, 49% strand | I3LCB2 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 114 | 8% helix, 31% strand | P60899 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 64 | 44% helix, 5% strand | A0A4X1VYD0 |
| K | DNA-directed RNA polymerase II subunit RPB11-a | protein | 115 | 42% helix, 23% strand | F1RKE4 |
| L | RNA polymerase II subunit K | protein | 44 | 0% helix, 27% strand | I3LN51 |
| M | Transcription initiation factor IIB (EC 2.3.1.48) | protein | 252 | 58% helix, 4% strand | Q00403 |
| N | Non-template DNA | dna | 198 | — | — |
| O | TATA-box-binding protein | protein | 179 | 27% helix, 34% strand | P20226 |
| Q | General transcription factor IIF subunit 1 | protein | 138 | 18% helix, 38% strand | P35269 |
| R | General transcription factor IIF subunit 2 (EC 3.6.4.12) | protein | 222 | 36% helix, 30% strand | P13984 |
| T | Template DNA | dna | 198 | — | — |
| U | Transcription initiation factor IIA subunit 1 | protein | 113 | 37% helix, 34% strand | P52655 |
| V | Transcription initiation factor IIA subunit 2 | protein | 99 | 37% helix, 37% strand | P52657 |
| a | Histone H3.2 | protein | 97 | 68% helix, 4% strand | P84233 |
| b, f | Histone H4 | protein | 82 | 60% helix, 7% strand | P62799 |
| c | Histone H2A type 1 | protein | 109 | 54% helix, 6% strand | P06897 |
| d | Histone H2B 1.1 | protein | 97 | 71% helix, 4% strand | P02281 |
| e | Histone H3.2 | protein | 98 | 66% helix, 4% strand | P84233 |
| g | Histone H2A type 1 | protein | 106 | 53% helix, 6% strand | P06897 |
| h | Histone H2B 1.1 | protein | 95 | 75% helix, 4% strand | P02281 |
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 | 1073 | 0.89 | 0.91 | 138 | empty |
| 2 | 926 | 0.82 | 0.84 | 95 | empty |
| 3 | 734 | 0.81 | 0.85 | 62 | empty |
| 4 | 946 | 0.80 | 0.82 | 105 | empty |
| 5 | 1130 | 0.80 | 0.81 | 116 | empty |
Interfaces
85 interfaces between chains.
- N–T · 9179 Ų buried · 1,054 hydrogen bonds · nucleic-nucleic
- A–B · 8958 Ų buried · 123 hydrogen bonds · protein-protein
- U–V · 2726 Ų buried · 38 hydrogen bonds · protein-protein
- g–h · 2618 Ų buried · 28 hydrogen bonds · protein-protein
- c–d · 2617 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- P84233 · AlphaFold monomer V2.0 prediction for histone H3.2 (P84233) · a predicted model of the same protein · chain e against A, TM-score 0.99
- P20226 · AlphaFold monomer V2.0 prediction for tata-box-binding protein (P20226) · a predicted model of the same protein · chain O against A, TM-score 0.99
- P62799 · AlphaFold monomer V2.0 prediction for histone H4 (P62799) · a predicted model of the same protein · chain b against A, TM-score 0.97
- P06897 · AlphaFold monomer V2.0 prediction for histone H2A type 1 (P06897) · a predicted model of the same protein · chain g against A, TM-score 0.96
- P52657 · AlphaFold monomer V2.0 prediction for transcription initiation factor iia subunit 2… · a predicted model of the same protein · chain V against A, TM-score 0.95
- Q00403 · AlphaFold monomer V2.0 prediction for transcription initiation factor iib (Q00403) · a predicted model of the same protein · chain M against A, TM-score 0.92
- P60899 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase II subunit RPB9 (P60899) · a predicted model of the same protein · chain I against A, TM-score 0.87
- P35269 · AlphaFold monomer V2.0 prediction for general transcription factor iif subunit 1 (P35269) · a predicted model of the same protein · chain Q against A, TM-score 0.76
- P52655 · AlphaFold monomer V2.0 prediction for transcription initiation factor iia subunit 1… · a predicted model of the same protein · chain U against A, TM-score 0.72
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 A0A8D1DPV6
- Every structure of UniProt I3LGP4
- Every structure of UniProt I3LCH3
- Every structure of UniProt A0A287ADR4
- Every structure of UniProt I3LSI7
- Every structure of UniProt F1SKN8
- Every structure of UniProt I3LJZ9
- Every structure of UniProt I3LCB2
- Every structure of UniProt P60899
- Every structure of UniProt A0A4X1VYD0
- Every structure of UniProt F1RKE4
- Every structure of UniProt I3LN51
- Every structure of UniProt Q00403
- Every structure of UniProt P20226
- Every structure of UniProt P35269
- Every structure of UniProt P13984
- Every structure of UniProt P52655
- Every structure of UniProt P52657
- Every structure of UniProt P84233
- Every structure of UniProt P62799
- Every structure of UniProt P06897
- Every structure of UniProt P02281
- Elsewhere: RCSB PDB 8BZ1 · PDBe 8BZ1 · UniProt A0A8D1DPV6 · UniProt I3LGP4 · UniProt I3LCH3 · UniProt A0A287ADR4 · UniProt I3LSI7 · UniProt F1SKN8 · UniProt I3LJZ9 · UniProt I3LCB2 · UniProt P60899 · UniProt A0A4X1VYD0 · UniProt F1RKE4 · UniProt I3LN51 · UniProt Q00403 · UniProt P20226 · UniProt P35269 · UniProt P13984 · UniProt P52655 · UniProt P52657 · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281
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