MolNFT v2 · #214539 · protein
Cryo-EM structure of human 26S proteasomal RP subcomplex (Ea state) without any bound substrate.
8JRI · 26S protease regulatory subunit 7: “Cryo-EM structure of human 26S proteasomal RP subcomplex (Ea state) without any bound substrate.”. Electron microscopy at 3.4, 3 ligands (ATP, ADP, MG), 20 pockets (best druggability 0.87). MolNFT…
- PDB
- 8JRI
- Type
- protein
- Length
- 8,787 residues
- Chains
- 25
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.4
- Source
- Homo sapiens
- Molecule
- 26S protease regulatory subunit 7; 26S protease regulatory subunit 4; 26S protease…
- EC
- 3.4.25.1, 3.4.19.-
- UniProt
- P35998, P62191, P62195, P43686, P60900, P25787, P25789, O14818, P28066, P25786, P25788, Q99460, O00487, O43242, O00232, O00231, Q15008, P51665, Q9UNM6, P55036, P48556, P60896, Q13200, P62333, P17980
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 3.4 · 25 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 26S protease regulatory subunit 7 | protein | 394 | 39% helix, 12% strand | P35998 |
| B | 26S protease regulatory subunit 4 | protein | 384 | 41% helix, 15% strand | P62191 |
| C | 26S protease regulatory subunit 8 | protein | 379 | 45% helix, 15% strand | P62195 |
| D | 26S protease regulatory subunit 6B | protein | 380 | 43% helix, 14% strand | P43686 |
| G | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 240 | 38% helix, 27% strand | P60900 |
| H | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 232 | 33% helix, 26% strand | P25787 |
| I | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 250 | 35% helix, 19% strand | P25789 |
| J | Proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 239 | 34% helix, 23% strand | O14818 |
| K | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 234 | 26% helix, 24% strand | P28066 |
| L | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 238 | 32% helix, 22% strand | P25786 |
| M | Proteasome subunit alpha type-3 | protein | 240 | 31% helix, 27% strand | P25788 |
| U | 26S proteasome non-ATPase regulatory subunit 1 | protein | 804 | 62% helix, 3% strand | Q99460 |
| c | 26S proteasome non-ATPase regulatory subunit 14 (EC 3.4.19.-) | protein | 287 | 42% helix, 16% strand | O00487 |
| V | 26S proteasome non-ATPase regulatory subunit 3 | protein | 508 | 58% helix, 1% strand | O43242 |
| W | 26S proteasome non-ATPase regulatory subunit 12 | protein | 456 | 63% helix, 2% strand | O00232 |
| X | 26S proteasome non-ATPase regulatory subunit 11 | protein | 380 | 69% helix, 3% strand | O00231 |
| Y | 26S proteasome non-ATPase regulatory subunit 6 | protein | 378 | 69% helix, 2% strand | Q15008 |
| Z | 26S proteasome non-ATPase regulatory subunit 7 | protein | 286 | 45% helix, 21% strand | P51665 |
| a | 26S proteasome non-ATPase regulatory subunit 13 | protein | 373 | 66% helix, 4% strand | Q9UNM6 |
| b | 26S proteasome non-ATPase regulatory subunit 4 | protein | 191 | 39% helix, 20% strand | P55036 |
| d | 26S proteasome non-ATPase regulatory subunit 8 | protein | 244 | 55% helix, 1% strand | P48556 |
| e | 26S proteasome complex subunit DSS1 | protein | 40 | 38% helix, 0% strand | P60896 |
| f | 26S proteasome non-ATPase regulatory subunit 2 | protein | 878 | 49% helix, 1% strand | Q13200 |
| E | 26S protease regulatory subunit 10B | protein | 375 | 40% helix, 16% strand | P62333 |
| F | 26S protease regulatory subunit 6A | protein | 377 | 40% helix, 15% strand | P17980 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D, E, F
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains C, A, F
- MG · Magnesium ion · metal · 5 copies · chains A, B, D, E, F
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 | 827 | 0.87 | 0.90 | 127 | empty |
| 2 | 1041 | 0.83 | 0.84 | 115 | ATP, MG |
| 3 | 583 | 0.82 | 0.87 | 76 | empty |
| 4 | 905 | 0.81 | 0.83 | 99 | ADP, MG |
| 5 | 1048 | 0.81 | 0.82 | 81 | empty |
Interfaces
85 interfaces between chains.
- E–F · 3763 Ų buried · 20 hydrogen bonds · protein-protein
- c–Z · 3614 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 3410 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 3044 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 2719 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- P25786 · AlphaFold monomer V2.0 prediction for proteasome subunit alpha type-1 (P25786) · a predicted model of the same protein · chain L against A, TM-score 0.98
- P25788 · AlphaFold monomer V2.0 prediction for proteasome subunit alpha type-3 (P25788) · a predicted model of the same protein · chain M against A, TM-score 0.97
- Q99460 · AlphaFold monomer V2.0 prediction for 26S proteasome non-ATPase regulatory subunit 1… · a predicted model of the same protein · chain U against A, TM-score 0.95
- P28066 · AlphaFold monomer V2.0 prediction for proteasome subunit alpha type-5 (P28066) · a predicted model of the same protein · chain K against A, TM-score 0.95
- P55036 · AlphaFold monomer V2.0 prediction for 26S proteasome non-ATPase regulatory subunit 4… · a predicted model of the same protein · chain b against A, TM-score 0.94
- P25787 · AlphaFold monomer V2.0 prediction for proteasome subunit alpha type-2 (P25787) · a predicted model of the same protein · chain H against A, TM-score 0.94
- O14818 · AlphaFold monomer V2.0 prediction for proteasome subunit alpha type-7 (O14818) · a predicted model of the same protein · chain J against A, TM-score 0.94
- O00487 · AlphaFold monomer V2.0 prediction for 26S proteasome non-ATPase regulatory subunit 14… · a predicted model of the same protein · chain c against A, TM-score 0.90
- P62333 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit 10B (P62333) · a predicted model of the same protein · chain E against A, TM-score 0.89
- Q15008 · AlphaFold monomer V2.0 prediction for 26S proteasome non-ATPase regulatory subunit 6… · a predicted model of the same protein · chain Y against A, TM-score 0.89
- Q9UNM6 · AlphaFold monomer V2.0 prediction for 26S proteasome non-ATPase regulatory subunit 13… · a predicted model of the same protein · chain a against A, TM-score 0.89
- Q13200 · AlphaFold monomer V2.0 prediction for 26S proteasome non-ATPase regulatory subunit 2… · a predicted model of the same protein · chain f against A, TM-score 0.87
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 P35998
- Every structure of UniProt P62191
- Every structure of UniProt P62195
- Every structure of UniProt P43686
- Every structure of UniProt P60900
- Every structure of UniProt P25787
- Every structure of UniProt P25789
- Every structure of UniProt O14818
- Every structure of UniProt P28066
- Every structure of UniProt P25786
- Every structure of UniProt P25788
- Every structure of UniProt Q99460
- Every structure of UniProt O00487
- Every structure of UniProt O43242
- Every structure of UniProt O00232
- Every structure of UniProt O00231
- Every structure of UniProt Q15008
- Every structure of UniProt P51665
- Every structure of UniProt Q9UNM6
- Every structure of UniProt P55036
- Every structure of UniProt P48556
- Every structure of UniProt P60896
- Every structure of UniProt Q13200
- Every structure of UniProt P62333
- Every structure of UniProt P17980
- Elsewhere: RCSB PDB 8JRI · PDBe 8JRI · UniProt P35998 · UniProt P62191 · UniProt P62195 · UniProt P43686 · UniProt P60900 · UniProt P25787 · UniProt P25789 · UniProt O14818 · UniProt P28066 · UniProt P25786 · UniProt P25788 · UniProt Q99460 · UniProt O00487 · UniProt O43242 · UniProt O00232 · UniProt O00231 · UniProt Q15008 · UniProt P51665 · UniProt Q9UNM6 · UniProt P55036 · UniProt P48556 · UniProt P60896 · UniProt Q13200 · UniProt P62333 · UniProt P17980
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