Research workbench
Yeast RNA polymerase I elongation complex at 3.8A
Analyse Yeast RNA polymerase I elongation complex at 3.8A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M3F
- Type
- protein + DNA + RNA
- Length
- 4,208 residues
- Chains
- 17
- 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, P20434, P20435, P20436, P32529, P22139, P28000, P40422, Q01080, P47006, P50106, P46669
- Ligands
- ZN, MG, SO4
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 17 distinct chains · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase I subunit RPA190 (EC 2.7.7.6) | protein | 1459 | 41% helix, 13% strand | P10964 |
| B | DNA-directed RNA polymerase I subunit RPA135 (EC 2.7.7.6) | protein | 1177 | 25% helix, 24% strand | P22138 |
| C | DNA-directed RNA polymerases I and III subunit RPAC1 | protein | 305 | 29% helix, 31% strand | P07703 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 212 | 37% helix, 20% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 100 | 51% helix, 13% strand | P20435 |
| 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 | 0% helix, 21% strand | P32529 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 69 | 42% helix, 1% strand | P22139 |
| K | DNA-directed RNA polymerases I and III subunit RPAC2 | protein | 101 | 40% helix, 23% strand | P28000 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 44 | 0% helix, 30% strand | P40422 |
| T | Template DNA | dna | 25 | — | — |
| U | Non-template DNA | dna | 14 | — | — |
| R | RNA | rna | 8 | — | — |
| M | DNA-directed RNA polymerase I subunit RPA49 | protein | 108 | 6% helix, 54% strand | Q01080 |
| N | DNA-directed RNA polymerase I subunit RPA34 | protein | 145 | 8% helix, 27% strand | P47006 |
| D | DNA-directed RNA polymerase I subunit RPA14 | protein | 54 | 54% helix, 11% strand | P50106 |
| G | DNA-directed RNA polymerase I subunit RPA43 | protein | 193 | 8% helix, 44% strand | P46669 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, I, J, L
- MG · Magnesium ion · metal · chains A, R
- 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 | 646 | 0.84 | 0.88 | 87 | empty |
| 2 | 1000 | 0.83 | 0.84 | 86 | empty |
| 3 | 884 | 0.82 | 0.84 | 90 | empty |
| 4 | 545 | 0.82 | 0.88 | 68 | empty |
| 5 | 637 | 0.81 | 0.86 | 85 | empty |
Interfaces
39 interfaces between chains.
- A–B · 9277 Ų buried · 93 hydrogen bonds · protein-protein
- A–E · 2685 Ų buried · 25 hydrogen bonds · protein-protein
- M–N · 2476 Ų buried · 34 hydrogen bonds · protein-protein
- A–F · 2136 Ų buried · 12 hydrogen bonds · protein-protein
- C–K · 2122 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 5M3F · Yeast RNA polymerase I elongation complex at 3.8A · the same entry in another collection · chain T against T, 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 P10964
- Every structure of UniProt P22138
- Every structure of UniProt P07703
- Every structure of UniProt P20434
- Every structure of UniProt P20435
- 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 P50106
- Every structure of UniProt P46669
- Elsewhere: RCSB PDB 5M3F · PDBe 5M3F · UniProt P10964 · UniProt P22138 · UniProt P07703 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P32529 · UniProt P22139 · UniProt P28000 · UniProt P40422 · UniProt Q01080 · UniProt P47006 · UniProt P50106 · UniProt P46669
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