MolNFT v1 · #138018 · protein + DNA + RNA
RNA polymerase I initial transcribing complex state 1
5W64 · DNA-directed RNA polymerase I subunit RPA190: “RNA polymerase I initial transcribing complex state 1”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.87). MolNFT v1 #138018 on GenesisL1: 3D structure, binding…
- PDB
- 5W64
- Type
- protein + DNA + RNA
- Length
- 5,660 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase I subunit RPA190; DNA-directed RNA polymerase I subunit…
- EC
- 2.7.7.6
- UniProt
- P10964, P22138, P07703, P50106, P20434, P20435, P46669, P20436, P32529, P22139, P28000, P40422, Q01080, P47006, P32786, P40992, Q04712
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 20 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase I subunit RPA190 (EC 2.7.7.6) | protein | 1461 | 46% helix, 14% strand | P10964 |
| B | DNA-directed RNA polymerase I subunit RPA135 (EC 2.7.7.6) | protein | 1178 | 31% helix, 26% strand | P22138 |
| C | DNA-directed RNA polymerases I and III subunit RPAC1 | protein | 306 | 30% helix, 32% strand | P07703 |
| D | DNA-directed RNA polymerase I subunit RPA14 | protein | 59 | 51% helix, 8% strand | P50106 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 215 | 43% helix, 23% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 83 | 36% helix, 17% strand | P20435 |
| G | DNA-directed RNA polymerase I subunit RPA43 | protein | 201 | 14% helix, 45% strand | P46669 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 133 | 5% helix, 52% strand | P20436 |
| I | DNA-directed RNA polymerase I subunit RPA12 | protein | 65 | 8% helix, 14% strand | P32529 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 69 | 48% helix, 4% strand | P22139 |
| K | DNA-directed RNA polymerases I and III subunit RPAC2 | protein | 103 | 47% helix, 24% strand | P28000 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 45 | 0% helix, 24% strand | P40422 |
| M | DNA-directed RNA polymerase I subunit RPA49 | protein | 106 | 7% helix, 44% strand | Q01080 |
| N | DNA-directed RNA polymerase I subunit RPA34 | protein | 158 | 9% helix, 23% strand | P47006 |
| O | RNA polymerase I-specific transcription initiation factor RRN6 | protein | 640 | 20% helix, 18% strand | P32786 |
| P | RNA polymerase I-specific transcription initiation factor RRN7 | protein | 387 | 59% helix, 0% strand | P40992 |
| Q | RNA polymerase I-specific transcription initiation factor RRN11 | protein | 349 | 55% helix, 0% strand | Q04712 |
| R | RNA | rna | 6 | — | — |
| S | Non-template strand DNA | dna | 42 | — | — |
| T | Template strand DNA | dna | 54 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, I, J, L
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 | 878 | 0.87 | 0.90 | 96 | empty |
| 2 | 1111 | 0.84 | 0.86 | 106 | empty |
| 3 | 1150 | 0.84 | 0.85 | 124 | empty |
| 4 | 666 | 0.84 | 0.88 | 81 | empty |
| 5 | 459 | 0.83 | 0.90 | 76 | empty |
Interfaces
50 interfaces between chains.
- A–B · 8836 Ų buried · 137 hydrogen bonds · protein-protein
- O–P · 4514 Ų buried · 44 hydrogen bonds · protein-protein
- O–Q · 3884 Ų buried · 56 hydrogen bonds · protein-protein
- A–E · 2580 Ų buried · 30 hydrogen bonds · protein-protein
- M–N · 2482 Ų buried · 50 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 isopeptide (disulfide, isopeptide).
Compared structures
- P22138 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase I subunit RPA135… · a predicted model of the same protein · chain B against A, TM-score 0.98
- P10964 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase I subunit RPA190… · a predicted model of the same protein · chain A against A, TM-score 0.97
- P07703 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerases I and III subunit… · a predicted model of the same protein · chain C against A, TM-score 0.96
- P28000 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerases I and III subunit… · a predicted model of the same protein · chain K against A, TM-score 0.95
- P40992 · AlphaFold monomer V2.0 prediction for RNA polymerase I-specific transcription initiation… · a predicted model of the same protein · chain P against A, TM-score 0.92
- P32786 · AlphaFold monomer V2.0 prediction for RNA polymerase I-specific transcription initiation… · a predicted model of the same protein · chain O against A, TM-score 0.90
- P46669 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase I subunit RPA43 (P46669) · a predicted model of the same protein · chain G against A, TM-score 0.89
- Q01080 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase I subunit RPA49 (Q01080) · a predicted model of the same protein · chain M against A, TM-score 0.82
- P50106 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase I subunit RPA14 (P50106) · a predicted model of the same protein · chain D against A, TM-score 0.77
- Q04712 · AlphaFold monomer V2.0 prediction for RNA polymerase I-specific transcription initiation… · a predicted model of the same protein · chain Q against A, TM-score 0.70
- P32529 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase I subunit RPA12 (P32529) · a predicted model of the same protein · chain I against A, TM-score 0.69
- P47006 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase I subunit RPA34 (P47006) · a predicted model of the same protein · chain N against A, TM-score 0.64
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 P10964
- Every structure of UniProt P22138
- Every structure of UniProt P07703
- Every structure of UniProt P50106
- Every structure of UniProt P20434
- Every structure of UniProt P20435
- Every structure of UniProt P46669
- Every structure of UniProt P20436
- Every structure of UniProt P32529
- Every structure of UniProt P22139
- Every structure of UniProt P28000
- Every structure of UniProt P40422
- Every structure of UniProt Q01080
- Every structure of UniProt P47006
- Every structure of UniProt P32786
- Every structure of UniProt P40992
- Every structure of UniProt Q04712
- Elsewhere: RCSB PDB 5W64 · PDBe 5W64 · UniProt P10964 · UniProt P22138 · UniProt P07703 · UniProt P50106 · UniProt P20434 · UniProt P20435 · UniProt P46669 · UniProt P20436 · UniProt P32529 · UniProt P22139 · UniProt P28000 · UniProt P40422 · UniProt Q01080 · UniProt P47006 · UniProt P32786 · UniProt P40992 · UniProt Q04712
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