Research workbench
RNA polymerase II core pre-initiation complex with closed promoter DNA in distal position
Analyse RNA polymerase II core pre-initiation complex with closed promoter DNA in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NVT
- Type
- protein + DNA
- Length
- 5,349 residues
- Chains
- 22
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RPB1; DNA-directed RNA polymerase subunit beta; DNA-directed RNA polymerase II subunit…
- EC
- 2.7.7.6, 2.3.1.48, 3.6.4.12
- UniProt
- I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, F1SKN8, I3LJZ9, A0A4X1ULF2, P60899, A0A4X1VYD0, A0A4X1UK25, I3LN51, Q00403, P20226, P35269, P13984, P52655, P52657, P29083, P29084
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 22 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RPB1 | protein | 1423 | 43% helix, 15% strand | — |
| B | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1136 | 30% helix, 25% strand | I3LGP4 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 257 | 25% helix, 28% strand | I3LCH3 |
| D | RPOL4C domain-containing protein | protein | 128 | 62% helix, 3% strand | A0A287ADR4 |
| E | DNA-directed RNA polymerase II subunit E | protein | 209 | 40% helix, 24% strand | I3LSI7 |
| F | DNA-directed RNA polymerase II subunit F | protein | 79 | 38% helix, 16% strand | F1SKN8 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 9% helix, 50% strand | I3LJZ9 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 148 | 3% helix, 49% strand | A0A4X1ULF2 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 114 | 8% helix, 33% strand | P60899 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 64 | 44% helix, 5% strand | A0A4X1VYD0 |
| K | RNA_POL_L_2 domain-containing protein | protein | 115 | 43% helix, 23% strand | A0A4X1UK25 |
| 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 | 50 | — | — |
| O | Tata-box-binding protein | protein | 179 | 27% helix, 34% strand | P20226 |
| Q | General transcription factor iif subunit 1 | protein | 138 | 16% helix, 37% strand | P35269 |
| R | General transcription factor iif subunit 2 (EC 3.6.4.12) | protein | 222 | 34% helix, 28% strand | P13984 |
| T | Template DNA | dna | 50 | — | — |
| U | Transcription initiation factor iia subunit 1 | protein | 113 | 36% helix, 34% strand | P52655 |
| V | Transcription initiation factor iia subunit 2 | protein | 99 | 37% helix, 36% strand | P52657 |
| W | General transcription factor iie subunit 1 | protein | 187 | 59% helix, 16% strand | P29083 |
| X | Transcription initiation factor iie subunit beta | protein | 171 | 52% helix, 11% strand | P29084 |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains A, B, C, I, J, L, M, W
- MG · Magnesium ion · metal · chains A
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 | 1162 | 0.87 | 0.88 | 125 | empty |
| 2 | 959 | 0.84 | 0.85 | 130 | empty |
| 3 | 1052 | 0.83 | 0.84 | 84 | empty |
| 4 | 948 | 0.80 | 0.82 | 90 | empty |
| 5 | 562 | 0.80 | 0.86 | 54 | empty |
Interfaces
57 interfaces between chains.
- A–B · 8876 Ų buried · 125 hydrogen bonds · protein-protein
- U–V · 2772 Ų buried · 39 hydrogen bonds · protein-protein
- Q–R · 2395 Ų buried · 42 hydrogen bonds · protein-protein
- A–E · 2328 Ų buried · 29 hydrogen bonds · protein-protein
- C–K · 2260 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7NVT · RNA polymerase II core pre-initiation complex with closed promoter DNA in distal position · the same entry in another collection · chain I against I, TM-score 1.00
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 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 A0A4X1ULF2
- Every structure of UniProt P60899
- Every structure of UniProt A0A4X1VYD0
- Every structure of UniProt A0A4X1UK25
- 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 P29083
- Every structure of UniProt P29084
- Elsewhere: RCSB PDB 7NVT · PDBe 7NVT · UniProt I3LGP4 · UniProt I3LCH3 · UniProt A0A287ADR4 · UniProt I3LSI7 · UniProt F1SKN8 · UniProt I3LJZ9 · UniProt A0A4X1ULF2 · UniProt P60899 · UniProt A0A4X1VYD0 · UniProt A0A4X1UK25 · UniProt I3LN51 · UniProt Q00403 · UniProt P20226 · UniProt P35269 · UniProt P13984 · UniProt P52655 · UniProt P52657 · UniProt P29083 · UniProt P29084
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