Research workbench
RNA polymerase II pre-initiation complex with closed promoter DNA in distal position
Analyse RNA polymerase II pre-initiation complex with closed promoter DNA in distal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NVZ
- Type
- protein + DNA
- Length
- 8,218 residues
- Chains
- 32
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tfiih basal transcription factor complex helicase xpd subunit; General transcription…
- EC
- 3.6.4.12, 2.7.7.6, 2.3.1.48
- UniProt
- P18074, P32780, Q92759, P51948, Q13889, Q6ZYL4, Q13888, P19447, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, F1SKN8, I3LJZ9, A0A4X1ULF2, P60899, A0A4X1VYD0, A0A4X1UK25, I3LN51, Q00403, P20226, P35269, P13984, P52655, P52657, P29083, P29084
- Ligands
- SF4, ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 32 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | Tfiih basal transcription factor complex helicase xpd subunit (EC 3.6.4.12) | protein | 714 | 51% helix, 12% strand | P18074 |
| 1 | General transcription factor iih subunit 1 | protein | 265 | 68% helix, 0% strand | P32780 |
| 2 | General transcription factor iih subunit 4 | protein | 390 | 55% helix, 12% strand | Q92759 |
| 3 | Cdk-activating kinase assembly factor MAT1 | protein | 149 | 54% helix, 5% strand | P51948 |
| 4 | General transcription factor iih subunit 3 | protein | 263 | 41% helix, 15% strand | Q13889 |
| 5 | General transcription factor iih subunit 5 | protein | 66 | 45% helix, 24% strand | Q6ZYL4 |
| 6 | General transcription factor iih subunit 2 | protein | 347 | 32% helix, 19% strand | Q13888 |
| 7 | General transcription and DNA repair factor iih helicase subunit xpb (EC 3.6.4.12) | protein | 605 | 40% helix, 17% strand | P19447 |
| 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 | 26% helix, 28% strand | I3LCH3 |
| D | RPOL4C domain-containing protein | protein | 128 | 61% helix, 3% strand | A0A287ADR4 |
| E | DNA-directed RNA polymerase II subunit E | protein | 209 | 39% helix, 24% strand | I3LSI7 |
| F | DNA-directed RNA polymerase II subunit F | protein | 79 | 33% 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, 47% 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 | 45% helix, 5% strand | A0A4X1VYD0 |
| K | RNA_POL_L_2 domain-containing protein | protein | 115 | 42% 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 | 59% helix, 4% strand | Q00403 |
| N | Non-template DNA | dna | 64 | — | — |
| O | Tata-box-binding protein | protein | 179 | 27% helix, 35% strand | P20226 |
| Q | General transcription factor iif subunit 1 | protein | 138 | 17% helix, 37% strand | P35269 |
| R | General transcription factor iif subunit 2 (EC 3.6.4.12) | protein | 222 | 34% helix, 29% strand | P13984 |
| T | Template DNA | dna | 64 | — | — |
| 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 | 202 | 55% helix, 14% strand | P29083 |
| X | Transcription initiation factor iie subunit beta | protein | 171 | 53% helix, 11% strand | P29084 |
| Y | Unassigned peptide, likely tfiie-beta | protein | 19 | 16% helix, 0% strand | — |
| Z | Unassigned peptide, likely xpb | protein | 8 | 0% helix, 25% strand | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains 0
- ZN · Zinc ion · metal · 17 copies · chains 3, 4, 6, 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 | 1099 | 0.89 | 0.90 | 132 | empty |
| 2 | 998 | 0.83 | 0.84 | 70 | empty |
| 3 | 902 | 0.82 | 0.84 | 121 | empty |
| 4 | 1089 | 0.81 | 0.82 | 122 | empty |
| 5 | 184 | 0.81 | 0.96 | 31 | empty |
Interfaces
81 interfaces between chains.
- A–B · 8887 Ų buried · 128 hydrogen bonds · protein-protein
- N–T · 2868 Ų buried · 225 hydrogen bonds · nucleic-nucleic
- U–V · 2768 Ų buried · 38 hydrogen bonds · protein-protein
- 4–6 · 2501 Ų buried · 17 hydrogen bonds · protein-protein
- Q–R · 2390 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7NVZ · RNA polymerase II pre-initiation complex with closed promoter DNA in distal position · the same entry in another collection · chain C against C, 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 P18074
- Every structure of UniProt P32780
- Every structure of UniProt Q92759
- Every structure of UniProt P51948
- Every structure of UniProt Q13889
- Every structure of UniProt Q6ZYL4
- Every structure of UniProt Q13888
- Every structure of UniProt P19447
- 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 7NVZ · PDBe 7NVZ · UniProt P18074 · UniProt P32780 · UniProt Q92759 · UniProt P51948 · UniProt Q13889 · UniProt Q6ZYL4 · UniProt Q13888 · UniProt P19447 · 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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