Research workbench
Architecture of the RNA polymerase II-mediator core transcription initiation complex
Analyse Architecture of the RNA polymerase II-mediator core transcription initiation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4V1O
- Type
- protein + DNA + RNA
- Length
- 6,126 residues
- Chains
- 26
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase II subunit RPB1; DNA-directed RNA polymerase II subunit RPB2…
- EC
- 2.7.7.6, 3.6.4.12
- UniProt
- P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41896, P38782, P38304, Q99278, P32569, P32585, P34162, P32570
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 26 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1422 | 41% helix, 17% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1156 | 28% helix, 26% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 266 | 26% helix, 29% strand | P16370 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 178 | 51% helix, 4% strand | P20433 |
| E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1 | protein | 214 | 41% helix, 24% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2 | protein | 84 | 35% helix, 15% strand | P20435 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 9% helix, 52% strand | P34087 |
| H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3 | protein | 133 | 2% helix, 43% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 119 | 4% helix, 30% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5 | protein | 65 | 45% helix, 2% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 114 | 40% helix, 24% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4 | protein | 46 | 0% helix, 13% strand | P40422 |
| M | Transcription initiation factor iib | protein | 299 | 43% helix, 6% strand | P29055 |
| N | Nontemplate DNA | dna | 50 | — | — |
| O | Tata-box-binding protein | protein | 180 | 27% helix, 34% strand | P13393 |
| P | RNA | rna | 6 | — | — |
| Q | Transcription initiation factor iif subunit alpha | protein | 122 | 10% helix, 39% strand | — |
| R | Transcription initiation factor iif subunit beta (EC 3.6.4.12) | protein | 105 | 11% helix, 48% strand | P41896 |
| S | Mediator of RNA polymerase II transcription subunit 6 | protein | 139 | 36% helix, 24% strand | P38782 |
| T | Template DNA | dna | 58 | — | — |
| U | Mediator of RNA polymerase II transcription subunit 8 | protein | 158 | 65% helix, 0% strand | P38304 |
| V | Mediator of RNA polymerase II transcription subunit 20 | protein | 99 | 82% helix, 2% strand | Q99278 |
| W | Mediator of RNA polymerase II transcription subunit 11 | protein | 419 | 49% helix, 19% strand | P32569 |
| X | Mediator of RNA polymerase II transcription subunit 18 | protein | 232 | 23% helix, 38% strand | P32585 |
| Y | Mediator of RNA polymerase II transcription subunit 20 | protein | 203 | 24% helix, 37% strand | P34162 |
| Z | Mediator of RNA polymerase II transcription subunit 22 | protein | 88 | 86% helix, 0% strand | P32570 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B, D, C, I, J, L, M
- MG · Magnesium ion · metal · chains A, P
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 | 995 | 0.89 | 0.91 | 115 | empty |
| 2 | 868 | 0.87 | 0.90 | 86 | empty |
| 3 | 1145 | 0.84 | 0.85 | 99 | empty |
| 4 | 1081 | 0.80 | 0.82 | 100 | empty |
| 5 | 605 | 0.80 | 0.85 | 55 | empty |
Interfaces
68 interfaces between chains.
- A–B · 9800 Ų buried · 156 hydrogen bonds · protein-protein
- A–M · 2667 Ų buried · 54 hydrogen bonds · protein-protein
- D–G · 2453 Ų buried · 31 hydrogen bonds · protein-protein
- N–T · 2291 Ų buried · 202 hydrogen bonds · nucleic-nucleic
- A–E · 2212 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 4V1O · Architecture of the RNA polymerase II-Mediator core transcription initiation complex · the same entry in another collection · chain K against K, 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 P04050
- Every structure of UniProt P08518
- Every structure of UniProt P16370
- Every structure of UniProt P20433
- Every structure of UniProt P20434
- Every structure of UniProt P20435
- Every structure of UniProt P34087
- Every structure of UniProt P20436
- Every structure of UniProt P27999
- Every structure of UniProt P22139
- Every structure of UniProt P38902
- Every structure of UniProt P40422
- Every structure of UniProt P29055
- Every structure of UniProt P13393
- Every structure of UniProt P41896
- Every structure of UniProt P38782
- Every structure of UniProt P38304
- Every structure of UniProt Q99278
- Every structure of UniProt P32569
- Every structure of UniProt P32585
- Every structure of UniProt P34162
- Every structure of UniProt P32570
- Elsewhere: RCSB PDB 4V1O · PDBe 4V1O · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20433 · UniProt P20434 · UniProt P20435 · UniProt P34087 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422 · UniProt P29055 · UniProt P13393 · UniProt P41896 · UniProt P38782 · UniProt P38304 · UniProt Q99278 · UniProt P32569 · UniProt P32585 · UniProt P34162 · UniProt P32570
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