Research workbench
Structure of the pre state human RNA Polymerase I Elongation Complex
Analyse Structure of the pre state human RNA Polymerase I Elongation Complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VBA
- Type
- protein + DNA + RNA
- Length
- 4,091 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.89
- Source
- Homo sapiens
- Molecule
- DNA-directed RNA polymerase I subunit RPA1; DNA-directed RNA polymerase I subunit RPA2…
- EC
- 2.7.7.6
- UniProt
- O95602, Q9H9Y6, O15160, P19388, P61218, P52434, Q9P1U0, P62875, P0DPB6, P53803, O15446, Q3B726, Q9GZS1
- Ligands
- 2TM, ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 2.89 · 16 distinct chains · 28% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase I subunit RPA1 (EC 2.7.7.6) | protein | 1473 | 40% helix, 10% strand | O95602 |
| B | DNA-directed RNA polymerase I subunit RPA2 (EC 2.7.7.6) | protein | 1123 | 24% helix, 23% strand | Q9H9Y6 |
| C | DNA-directed RNA polymerases I and III subunit RPAC1 | protein | 337 | 22% helix, 25% strand | O15160 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 199 | 35% helix, 24% strand | P19388 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 76 | 36% helix, 16% strand | P61218 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 146 | 2% helix, 45% strand | P52434 |
| I | DNA-directed RNA polymerase I subunit RPA12 | protein | 60 | 0% helix, 7% strand | Q9P1U0 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 64 | 44% helix, 5% strand | P62875 |
| K | DNA-directed RNA polymerases I and III subunit RPAC2 | protein | 108 | 42% helix, 26% strand | P0DPB6 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 45 | 0% helix, 29% strand | P53803 |
| N | DNA-directed RNA polymerase I subunit RPA34 | protein | 151 | 7% helix, 32% strand | O15446 |
| G | DNA-directed RNA polymerase I subunit RPA43 | protein | 157 | 8% helix, 25% strand | Q3B726 |
| M | DNA-directed RNA polymerase I subunit RPA49 | protein | 110 | 5% helix, 47% strand | Q9GZS1 |
| R | RNA (5'-R(P*UP*GP*CP*UP*GP*AP*CP*U)-3') | rna | 8 | — | — |
| T | DNA (5'-D(P*GP*CP*CP*AP*GP*AP*GP*AP*CP*AP*GP*CP*GP*AP*GP*TP*CP*AP*GP*CP*AP*A)-3') | dna | 22 | — | — |
| U | DNA (5'-D(P*A*CP*TP*GP*TP*CP*CP*TP*CP*TP*GP*GP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
- 2TM · 5'-O-[(S)-hydroxy{[(s)-hydroxy(phosphonooxy) phosphoryl]methyl}phosphoryl]cytidine · ligand · chains A, B, R, T
- ZN · Zinc ion · metal · 5 copies · chains A, B, J, L
- MG · Magnesium ion · metal · chains A, R
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 | 983 | 0.84 | 0.85 | 98 | empty |
| 2 | 805 | 0.83 | 0.86 | 118 | 2TM |
| 3 | 1053 | 0.82 | 0.83 | 71 | empty |
| 4 | 1086 | 0.82 | 0.83 | 121 | empty |
| 5 | 898 | 0.79 | 0.81 | 102 | empty |
Interfaces
38 interfaces between chains.
- A–B · 9111 Ų buried · 87 hydrogen bonds · protein-protein
- A–E · 3571 Ų buried · 47 hydrogen bonds · protein-protein
- N–M · 2553 Ų buried · 36 hydrogen bonds · protein-protein
- C–K · 2104 Ų buried · 21 hydrogen bonds · protein-protein
- A–H · 2100 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- Q9H9Y6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase I subunit RPA2 (Q9H9Y6) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P19388 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerases I, II, and III subunit… · a predicted model of the same protein · chain E against A, TM-score 0.98
- O15160 · 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 0.98
- P61218 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerases I, II, and III subunit… · a predicted model of the same protein · chain F against A, TM-score 0.96
- O95602 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase I subunit RPA1 (O95602) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P52434 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerases I, II, and III subunit… · a predicted model of the same protein · chain H against A, TM-score 0.95
- P62875 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerases I, II, and III subunit… · a predicted model of the same protein · chain J against A, TM-score 0.95
- P0DPB6 · 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 0.94
- Q9GZS1 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase I subunit RPA49 (Q9GZS1) · a predicted model of the same protein · chain M against A, TM-score 0.92
- P53803 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerases I, II, and III subunit… · a predicted model of the same protein · chain L against A, TM-score 0.77
- Q3B726 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase I subunit RPA43 (Q3B726) · a predicted model of the same protein · chain G against A, TM-score 0.73
- O15446 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase I subunit RPA34 (O15446) · a predicted model of the same protein · chain N against A, TM-score 0.70
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 O95602
- Every structure of UniProt Q9H9Y6
- Every structure of UniProt O15160
- Every structure of UniProt P19388
- Every structure of UniProt P61218
- Every structure of UniProt P52434
- Every structure of UniProt Q9P1U0
- Every structure of UniProt P62875
- Every structure of UniProt P0DPB6
- Every structure of UniProt P53803
- Every structure of UniProt O15446
- Every structure of UniProt Q3B726
- Every structure of UniProt Q9GZS1
- Elsewhere: RCSB PDB 7VBA · PDBe 7VBA · UniProt O95602 · UniProt Q9H9Y6 · UniProt O15160 · UniProt P19388 · UniProt P61218 · UniProt P52434 · UniProt Q9P1U0 · UniProt P62875 · UniProt P0DPB6 · UniProt P53803 · UniProt O15446 · UniProt Q3B726 · UniProt Q9GZS1
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