Research workbench
Cryo-EM structure of yeast apo RNA polymerase III at 4.6 A
Analyse Cryo-EM structure of yeast apo RNA polymerase III at 4.6 A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FJ9
- Type
- protein
- Length
- 4,880 residues
- Chains
- 17
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.6
- Source
- SACCHAROMYCES CEREVISIAE
- Molecule
- DNA-directed RNA polymerase III subunit RPC1; DNA-directed RNA polymerase III subunit…
- EC
- 2.7.7.6
- UniProt
- P04051, P22276, P07703, P47076, P20434, P20435, P35718, P20436, Q04307, P22139, P28000, P40422, P36121, P25441, P32349, P32910, P17890
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 4.6 · 17 distinct chains · 31% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase III subunit RPC1 (EC 2.7.7.6) | protein | 1412 | 37% helix, 10% strand | P04051 |
| B | DNA-directed RNA polymerase III subunit RPC2 (EC 2.7.7.6) | protein | 1114 | 26% helix, 21% strand | P22276 |
| C | DNA-directed RNA polymerases I and III subunit RPAC1 | protein | 335 | 20% helix, 27% strand | P07703 |
| D | DNA-directed RNA polymerase III subunit RPC9 | protein | 119 | 42% helix, 3% strand | P47076 |
| E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1 | protein | 215 | 30% helix, 17% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2 | protein | 83 | 31% helix, 8% strand | P20435 |
| G | DNA-directed RNA polymerase III subunit RPC8 | protein | 191 | 13% helix, 35% strand | P35718 |
| H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3 | protein | 140 | 0% helix, 46% strand | P20436 |
| I | DNA-directed RNA polymerase III subunit RPC10 | protein | 92 | 0% helix, 37% strand | Q04307 |
| J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5 | protein | 67 | 42% helix, 3% strand | P22139 |
| K | DNA-directed RNA polymerases I and III subunit RPAC2 | protein | 101 | 41% helix, 18% strand | P28000 |
| L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4 | protein | 45 | 0% helix, 22% strand | P40422 |
| M | DNA-directed RNA polymerase III subunit RPC5 | protein | 165 | 21% helix, 22% strand | P36121 |
| N | DNA-directed RNA polymerase III subunit RPC4 | protein | 105 | 24% helix, 24% strand | P25441 |
| O | DNA-directed RNA polymerase III subunit RPC3 | protein | 528 | 53% helix, 5% strand | P32349 |
| P | DNA-directed RNA polymerase III subunit RPC6 | protein | 98 | 20% helix, 6% strand | P32910 |
| Q | DNA-directed RNA polymerase III subunit RPC7 | protein | 70 | 41% helix, 0% strand | P17890 |
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 | 876 | 0.86 | 0.88 | 118 | empty |
| 2 | 959 | 0.84 | 0.85 | 91 | empty |
| 3 | 1022 | 0.83 | 0.84 | 129 | empty |
| 4 | 525 | 0.82 | 0.88 | 58 | empty |
| 5 | 846 | 0.81 | 0.83 | 80 | empty |
Interfaces
37 interfaces between chains.
- A–B · 8793 Ų buried · 78 hydrogen bonds · protein-protein
- A–O · 2898 Ų buried · 22 hydrogen bonds · protein-protein
- C–K · 2328 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 2286 Ų buried · 24 hydrogen bonds · protein-protein
- M–N · 2271 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5FJ9 · Cryo-EM structure of yeast apo RNA polymerase III at 4.6 a · the same entry in another collection · chain J against J, 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 P04051
- Every structure of UniProt P22276
- Every structure of UniProt P07703
- Every structure of UniProt P47076
- Every structure of UniProt P20434
- Every structure of UniProt P20435
- Every structure of UniProt P35718
- Every structure of UniProt P20436
- Every structure of UniProt Q04307
- Every structure of UniProt P22139
- Every structure of UniProt P28000
- Every structure of UniProt P40422
- Every structure of UniProt P36121
- Every structure of UniProt P25441
- Every structure of UniProt P32349
- Every structure of UniProt P32910
- Every structure of UniProt P17890
- Elsewhere: RCSB PDB 5FJ9 · PDBe 5FJ9 · UniProt P04051 · UniProt P22276 · UniProt P07703 · UniProt P47076 · UniProt P20434 · UniProt P20435 · UniProt P35718 · UniProt P20436 · UniProt Q04307 · UniProt P22139 · UniProt P28000 · UniProt P40422 · UniProt P36121 · UniProt P25441 · UniProt P32349 · UniProt P32910 · UniProt P17890
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