Research workbench
Cryo-EM structure of RNA polymerase I in complex with RRN3 and core factor (orientation III)
Analyse Cryo-EM structure of RNA polymerase I in complex with RRN3 and core factor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N5Y
- Type
- protein
- Length
- 5,973 residues
- Chains
- 18
- 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 0.84
Structure
electron microscopy · 18 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase I subunit RPA190 (EC 2.7.7.6) | protein | 1467 | 44% helix, 14% strand | P10964 |
| B | DNA-directed RNA polymerase I subunit RPA135 (EC 2.7.7.6) | protein | 1172 | 29% helix, 25% strand | P22138 |
| C | DNA-directed RNA polymerases I and III subunit RPAC1 | protein | 305 | 29% helix, 33% strand | P07703 |
| D | DNA-directed RNA polymerase I subunit RPA14 | protein | 58 | 50% helix, 10% strand | P50106 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 212 | 40% helix, 23% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 100 | 47% helix, 13% strand | P20435 |
| G | DNA-directed RNA polymerase I subunit RPA43 | protein | 193 | 8% helix, 44% strand | P46669 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 131 | 3% helix, 53% strand | P20436 |
| I | DNA-directed RNA polymerase I subunit RPA12 | protein | 99 | 11% helix, 30% strand | P32529 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 69 | 41% helix, 3% strand | P22139 |
| K | DNA-directed RNA polymerases I and III subunit RPAC2 | protein | 101 | 40% 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 | 7% helix, 54% strand | Q01080 |
| N | DNA-directed RNA polymerase I subunit RPA34 | protein | 145 | 8% helix, 28% strand | P47006 |
| O | RNA polymerase I-specific transcription initiation factor RRN3 | protein | 473 | 73% helix, 1% strand | P36070 |
| P | RNA polymerase I-specific transcription initiation factor RRN6 | protein | 583 | 24% helix, 28% strand | P32786 |
| Q | RNA polymerase I-specific transcription initiation factor RRN7 | protein | 410 | 54% helix, 1% strand | P40992 |
| R | RNA polymerase I-specific transcription initiation factor RRN11 | protein | 303 | 60% helix, 0% strand | Q04712 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, I, J, L, Q
- MG · Magnesium ion · metal · chains P, R
- SO4 · Sulfate ion · ion · 5 copies · chains P, Q, 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 | 472 | 0.84 | 0.91 | 92 | SO4 |
| 2 | 941 | 0.83 | 0.85 | 130 | empty |
| 3 | 658 | 0.83 | 0.87 | 92 | empty |
| 4 | 893 | 0.82 | 0.84 | 106 | empty |
| 5 | 981 | 0.82 | 0.83 | 99 | empty |
Interfaces
45 interfaces between chains.
- A–B · 9045 Ų buried · 132 hydrogen bonds · protein-protein
- P–Q · 4272 Ų buried · 31 hydrogen bonds · protein-protein
- P–R · 3620 Ų buried · 64 hydrogen bonds · protein-protein
- A–E · 2629 Ų buried · 32 hydrogen bonds · protein-protein
- M–N · 2478 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 isopeptide, 3 disulfide (isopeptide, disulfide).
Compared structures
- 5N5Y · Cryo-EM structure of RNA polymerase I in complex with Rrn3 and Core Factor (Orientation… · the same entry in another collection · chain H against H, 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 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 5N5Y · PDBe 5N5Y · 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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