MolNFT v1 · #127757 · protein + DNA + RNA
RNA polymerase I initially transcribing complex
5N61 · DNA-directed RNA polymerase I subunit RPA190: “RNA polymerase I initially transcribing complex”. Electron microscopy, 3 ligands (ZN, MG, SO4), 20 pockets (best druggability 0.89). MolNFT v1 #127757 on GenesisL1: 3D structure…
- PDB
- 5N61
- Type
- protein + DNA + RNA
- Length
- 5,966 residues
- Chains
- 21
- 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, P36070, P32786, P40992, Q04712
- Ligands
- ZN, MG, SO4
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 21 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase I subunit RPA190 (EC 2.7.7.6) | protein | 1459 | 46% helix, 12% strand | P10964 |
| B | DNA-directed RNA polymerase I subunit RPA135 (EC 2.7.7.6) | protein | 1177 | 30% helix, 24% strand | P22138 |
| C | DNA-directed RNA polymerases I and III subunit RPAC1 | protein | 305 | 27% helix, 28% strand | P07703 |
| D | DNA-directed RNA polymerase I subunit RPA14 | protein | 54 | 54% helix, 11% strand | P50106 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 212 | 40% helix, 22% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 100 | 43% helix, 12% strand | P20435 |
| G | DNA-directed RNA polymerase I subunit RPA43 | protein | 193 | 9% helix, 41% strand | P46669 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 131 | 6% helix, 53% strand | P20436 |
| I | DNA-directed RNA polymerase I subunit RPA12 | protein | 63 | 6% helix, 24% 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 | 101 | 41% helix, 25% strand | P28000 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 44 | 0% helix, 30% strand | P40422 |
| M | DNA-directed RNA polymerase I subunit RPA49 | protein | 108 | 9% helix, 51% strand | Q01080 |
| N | DNA-directed RNA polymerase I subunit RPA34 | protein | 129 | 3% helix, 25% strand | P47006 |
| O | RNA polymerase I-specific transcription initiation factor RRN3 | protein | 463 | 69% helix, 0% strand | P36070 |
| P | RNA polymerase I-specific transcription initiation factor RRN6 | protein | 587 | 23% helix, 29% strand | P32786 |
| Q | RNA polymerase I-specific transcription initiation factor RRN7 | protein | 389 | 54% helix, 2% strand | P40992 |
| R | RNA polymerase I-specific transcription initiation factor RRN11 | protein | 303 | 58% helix, 1% strand | Q04712 |
| S | Product RNA | rna | 5 | — | — |
| T | Template DNA | dna | 41 | — | — |
| U | Non-template DNA | dna | 33 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains A, B, I, J, L, Q
- MG · Magnesium ion · metal · chains A, S
- SO4 · Sulfate ion · ion · chains B
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 | 993 | 0.89 | 0.90 | 133 | empty |
| 2 | 1183 | 0.85 | 0.86 | 138 | empty |
| 3 | 953 | 0.84 | 0.85 | 113 | empty |
| 4 | 1000 | 0.83 | 0.84 | 123 | empty |
| 5 | 937 | 0.83 | 0.84 | 112 | empty |
Interfaces
57 interfaces between chains.
- A–B · 9017 Ų buried · 119 hydrogen bonds · protein-protein
- P–Q · 4421 Ų buried · 39 hydrogen bonds · protein-protein
- P–R · 3513 Ų buried · 39 hydrogen bonds · protein-protein
- A–E · 2762 Ų buried · 40 hydrogen bonds · protein-protein
- M–N · 2339 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
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
- 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 0.98
- P36070 · 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 0.98
- 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 0.97
- 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
- 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 0.94
- P32786 · 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 0.91
- 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 0.86
- P40992 · 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 0.85
- 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 0.78
- 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 0.76
- Q04712 · AlphaFold monomer V2.0 prediction for RNA polymerase I-specific transcription initiation… · a predicted model of the same protein · chain R against A, TM-score 0.71
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 P36070
- Every structure of UniProt P32786
- Every structure of UniProt P40992
- Every structure of UniProt Q04712
- Elsewhere: RCSB PDB 5N61 · PDBe 5N61 · 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 P36070 · UniProt P32786 · UniProt P40992 · UniProt Q04712
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