Research workbench
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CIII membrane domain)
Analyse Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CIII… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8BEL
- Type
- protein
- Length
- 2,054 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.25
- Source
- Arabidopsis thaliana
- Molecule
- Cytochrome b; Cytochrome b-c1 complex subunit Rieske-1, mitochondrial; Cytochrome c1 2…
- EC
- 7.1.1.8
- UniProt
- P42792, Q94JS0, Q9FKS5, Q9SG91, Q0WWE3, Q9LXJ2, Q94K78
- Ligands
- CDL, HEM, 3PH, PC7, PGT, UQ5, PTY, FES, Q7G, UQ7
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 2.25 · 10 distinct chains · 57% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, M | Cytochrome b | protein | 387 | 70% helix, 2% strand | P42792 |
| D, N | Cytochrome b-c1 complex subunit Rieske-1, mitochondrial (EC 7.1.1.8) | protein | 179 | 23% helix, 17% strand | Q94JS0 |
| E, O | Cytochrome c1 2, heme protein, mitochondrial | protein | 244 | 39% helix, 8% strand | Q9FKS5 |
| G | Cytochrome b-c1 complex subunit 8-1, mitochondrial | protein | 69 | 68% helix, 6% strand | Q9SG91 |
| H | Cytochrome b-c1 complex subunit 6-1, mitochondrial | protein | 64 | 69% helix, 0% strand | Q0WWE3 |
| I, S | Cytochrome b-c1 complex subunit 9, mitochondrial | protein | 57 | 70% helix, 0% strand | Q9LXJ2 |
| J | Cytochrome b-c1 complex subunit 10, mitochondrial | protein | 28 | 79% helix, 0% strand | Q94K78 |
| Q | Cytochrome b-c1 complex subunit 8-1, mitochondrial | protein | 68 | 69% helix, 6% strand | Q9SG91 |
| R | Cytochrome b-c1 complex subunit 6-1, mitochondrial | protein | 63 | 75% helix, 0% strand | Q0WWE3 |
| T | Cytochrome b-c1 complex subunit 10, mitochondrial | protein | 28 | 64% helix, 0% strand | Q94K78 |
Ligands and binding sites
- CDL · Cardiolipin · ligand · 7 copies · chains C, D, E, I, G, M, Q, N, O, S
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains C, E, M, O
- 3PH · 1,2-diacyl-glycerol-3-sn-phosphate · ligand · 6 copies · chains C, G, E, I, M, O, T, N
- PC7 · (7S)-4-hydroxy-N,N,N-trimethyl-9-oxo-7-[(palmitoyloxy) methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide · ligand · 5 copies · chains C, G, D, I, J, E, M, Q, N, S, T
- PGT · (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · 4 copies · chains C, E, G, M
- UQ5 · 2,3-dimethoxy-5-methyl-6-(3,11,15,19-tetramethyl-eicosa-2,6,10,14,18-pentaenyl)-[1,4]benzoquinone · ligand · 3 copies · chains C, M, N
- PTY · Phosphatidylethanolamine · ligand · 3 copies · chains C, I, J, M, Q, S, T
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains D, N
- Q7G · 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta, 17beta,25r)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside · ligand · 2 copies · chains M, D
- UQ7 · Ubiquinone-7 · ligand · chains C, D, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1115 | 0.85 | 0.85 | 123 | HEM, UQ5, UQ7 |
| 2 | 700 | 0.83 | 0.87 | 68 | HEM |
| 3 | 689 | 0.83 | 0.87 | 66 | HEM |
| 4 | 1006 | 0.83 | 0.83 | 95 | HEM, UQ5, PC7 |
| 5 | 372 | 0.74 | 0.85 | 47 | HEM |
Interfaces
32 interfaces between chains.
- C–E · 1671 Ų buried · 14 hydrogen bonds · protein-protein
- M–O · 1669 Ų buried · 12 hydrogen bonds · protein-protein
- E–H · 1283 Ų buried · 12 hydrogen bonds · protein-protein
- O–R · 1182 Ų buried · 13 hydrogen bonds · protein-protein
- D–M · 1170 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- P42792 · AlphaFold monomer V2.0 prediction for cytochrome B (P42792) · a predicted model of the same protein · chain M against A, TM-score 1.00
- Q9FKS5 · AlphaFold monomer V2.0 prediction for cytochrome C1 2, heme protein, mitochondrial… · a predicted model of the same protein · chain E against A, TM-score 0.99
- Q0WWE3 · AlphaFold monomer V2.0 prediction for cytochrome B-C1 complex subunit 6-1, mitochondrial… · a predicted model of the same protein · chain R against A, TM-score 0.95
- Q9SG91 · AlphaFold monomer V2.0 prediction for cytochrome B-C1 complex subunit 8-1, mitochondrial… · a predicted model of the same protein · chain G against A, TM-score 0.92
- Q9LXJ2 · AlphaFold monomer V2.0 prediction for cytochrome B-C1 complex subunit 9, mitochondrial… · a predicted model of the same protein · chain I against A, TM-score 0.84
- Q94K78 · AlphaFold monomer V2.0 prediction for cytochrome B-C1 complex subunit 10, mitochondrial… · a predicted model of the same protein · chain J against A, TM-score 0.77
- Q94JS0 · AlphaFold monomer V2.0 prediction for cytochrome B-C1 complex subunit rieske-1… · a predicted model of the same protein · chain D 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 P42792
- Every structure of UniProt Q94JS0
- Every structure of UniProt Q9FKS5
- Every structure of UniProt Q9SG91
- Every structure of UniProt Q0WWE3
- Every structure of UniProt Q9LXJ2
- Every structure of UniProt Q94K78
- Elsewhere: RCSB PDB 8BEL · PDBe 8BEL · UniProt P42792 · UniProt Q94JS0 · UniProt Q9FKS5 · UniProt Q9SG91 · UniProt Q0WWE3 · UniProt Q9LXJ2 · UniProt Q94K78
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