Research workbench
cryo-EM structure of human EMC and VDAC
Analyse cryo-EM structure of human EMC and VDAC in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8J0O
- Type
- protein
- Length
- 2,627 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.32
- Source
- Homo sapiens
- Molecule
- ER membrane protein complex subunit 1; ER membrane protein complex subunit 2; ER membrane…
- UniProt
- Q8N766, Q15006, Q9P0I2, Q5J8M3, Q8N4V1, Q9BV81, Q9NPA0, O43402, Q5UCC4, P21796
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · resolution 3.32 · 10 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ER membrane protein complex subunit 1 | protein | 949 | 10% helix, 40% strand | Q8N766 |
| B | ER membrane protein complex subunit 2 | protein | 296 | 81% helix, 0% strand | Q15006 |
| C | ER membrane protein complex subunit 3 | protein | 258 | 52% helix, 2% strand | Q9P0I2 |
| D | ER membrane protein complex subunit 4 | protein | 156 | 55% helix, 4% strand | Q5J8M3 |
| E | ER membrane protein complex subunit 5 | protein | 103 | 64% helix, 1% strand | Q8N4V1 |
| F | ER membrane protein complex subunit 6 | protein | 100 | 77% helix, 1% strand | Q9BV81 |
| G | ER membrane protein complex subunit 7 | protein | 139 | 14% helix, 32% strand | Q9NPA0 |
| H | ER membrane protein complex subunit 8 | protein | 195 | 36% helix, 25% strand | O43402 |
| J | ER membrane protein complex subunit 10 | protein | 149 | 17% helix, 39% strand | Q5UCC4 |
| K | Voltage-dependent anion-selective channel protein 1 | protein | 282 | 3% helix, 62% strand | P21796 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, J, G
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.80 | 0.81 | 100 | empty |
| 2 | 1039 | 0.80 | 0.81 | 106 | empty |
| 3 | 1191 | 0.79 | 0.80 | 112 | empty |
| 4 | 1027 | 0.78 | 0.79 | 85 | empty |
| 5 | 843 | 0.77 | 0.80 | 80 | empty |
Interfaces
24 interfaces between chains.
- A–G · 1737 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1726 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 1641 Ų buried · 5 hydrogen bonds · protein-protein
- A–J · 1618 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 1611 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan (N-glycosylation).
Compared structures
- P21796 · AlphaFold monomer V2.0 prediction for voltage-dependent anion- selective channel protein… · a predicted model of the same protein · chain K against A, TM-score 0.96
- Q8N766 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 1 (Q8N766) · a predicted model of the same protein · chain A against A, TM-score 0.94
- O43402 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 8 (O43402) · a predicted model of the same protein · chain H against A, TM-score 0.94
- Q5UCC4 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 10 (Q5UCC4) · a predicted model of the same protein · chain J against A, TM-score 0.90
- Q9BV81 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 6 (Q9BV81) · a predicted model of the same protein · chain F against A, TM-score 0.90
- Q15006 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 2 (Q15006) · a predicted model of the same protein · chain B against A, TM-score 0.89
- Q9NPA0 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 7 (Q9NPA0) · a predicted model of the same protein · chain G against A, TM-score 0.74
- Q5J8M3 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 4 (Q5J8M3) · a predicted model of the same protein · chain D against A, TM-score 0.69
- Q8N4V1 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 5 (Q8N4V1) · a predicted model of the same protein · chain E against A, TM-score 0.59
- Q9P0I2 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 3 (Q9P0I2) · a predicted model of the same protein · chain C against A, TM-score 0.57
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 Q8N766
- Every structure of UniProt Q15006
- Every structure of UniProt Q9P0I2
- Every structure of UniProt Q5J8M3
- Every structure of UniProt Q8N4V1
- Every structure of UniProt Q9BV81
- Every structure of UniProt Q9NPA0
- Every structure of UniProt O43402
- Every structure of UniProt Q5UCC4
- Every structure of UniProt P21796
- Elsewhere: RCSB PDB 8J0O · PDBe 8J0O · UniProt Q8N766 · UniProt Q15006 · UniProt Q9P0I2 · UniProt Q5J8M3 · UniProt Q8N4V1 · UniProt Q9BV81 · UniProt Q9NPA0 · UniProt O43402 · UniProt Q5UCC4 · UniProt P21796
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