Cryo-EM structure of ND6-P25L mutant respiratory complex I from mus musculus at 3.8 a

Structure

electron microscopy · 45 distinct chains · 50% helix, 6% strand (DSSP).

Ligands and binding sites

• SF4 · Iron/sulfur cluster · ligand · 6 copies · chains B, D, F, G, I
• 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 4 copies · chains D, H, I, Z, b, A, J, a, L, M, l, g
• FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, F, G
• CDL · Cardiolipin · ligand · 2 copies · chains L, M, h, N, X, d, f
• EHZ · ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate · ligand · 2 copies · chains T, W, U, n
• PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · chains B, H, q
• FMN · Flavin mononucleotide · ligand · chains F
• ATP · Adenosine-5'-triphosphate · ligand · chains O
• NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains B, P
• ZN · Zinc ion · metal · chains 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.

Interfaces

197 interfaces between chains.

• E–F · 2908 Ų buried · 25 hydrogen bonds · protein-protein
• C–D · 2748 Ų buried · 20 hydrogen bonds · protein-protein
• J–K · 2682 Ų buried · 10 hydrogen bonds · protein-protein
• A–H · 2519 Ų buried · 9 hydrogen bonds · protein-protein
• L–M · 2400 Ų buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 modified, 5 disulfide, 2 covalent (formylation, disulfide, covalent ligand, methylation, nonstandard).

Compared structures

• 7AK6 · Cryo-EM structure of ND6-P25L mutant respiratory complex I from Mus musculus at 3.8 A · the same entry in another collection · chain I against I, 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
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