Cryo-EM structure of a respiratory complex I

Structure

electron microscopy · 42 distinct chains · 53% helix, 8% strand (DSSP).

Ligands and binding sites

• 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 18 copies · chains S, 4, b, C, I, 1, g, W, 3, E, U, 2, 5, i, a, J, 6, D, K, j
• SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, C, B, I, K
• PLC · Diundecyl phosphatidyl choline · ligand · 6 copies · chains K, 1, D, h, g, W, C, 2, 4, 5, S, i, n, I
• CDL · Cardiolipin · ligand · 6 copies · chains 2, 3, g, X, 1, E, I, W, Z, 6, D, h, S, 4, 5, i, n
• T7X · Phosphatidylinositol · ligand · 3 copies · chains 2, X, b, L, 5, 6, J, K, 1, 3, E
• FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, H
• LMN · Lauryl Maltose Neopentyl Glycol · ligand · 2 copies · chains j, J, a, 2, 4
• ZMP · S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate · ligand · 2 copies · chains O, P, Q, R
• FMN · Flavin mononucleotide · ligand · chains B
• CPL · 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine · ligand · chains 2, b
• NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains K, E
• ZN · Zinc ion · metal · chains 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, 20 with a druggability of 0.5 or more.

Interfaces

197 interfaces between chains.

• B–H · 3388 Ų buried · 48 hydrogen bonds · protein-protein
• 1–3 · 3339 Ų buried · 13 hydrogen bonds · protein-protein
• L–6 · 3026 Ų buried · 18 hydrogen bonds · protein-protein
• G–Z · 2860 Ų buried · 33 hydrogen bonds · protein-protein
• C–G · 2735 Ų buried · 44 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide, 6 modified, 5 covalent (disulfide, covalent ligand, formylation, methylation).

Compared structures

• 7O71 · Cryo-EM structure of a respiratory complex I · the same entry in another collection · chain B against B, 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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• Elsewhere: RCSB PDB 7O71 · PDBe 7O71 · UniProt Q9UUU3 · UniProt Q9UUU2 · UniProt Q9UUU1 · UniProt Q9UUU0 · UniProt Q9UUT9 · UniProt Q9UUT8 · UniProt Q9UUT7 · UniProt S5U4U1 · UniProt Q6ZY23 · UniProt Q6ZY24 · UniProt S5U3V2 · UniProt S5U4R9 · UniProt S5TMS4 · UniProt S5TMP9 · UniProt S5TF58 · UniProt S5U3X7 · UniProt A0A1D8NJR0 · UniProt A0A1D8NC63 · UniProt A0A371BY45 · UniProt A0A371C5F3 · UniProt A0A371CB65 · UniProt A0A1H6Q8Z5 · UniProt A0A1H6PXT9 · UniProt A0A1D8N3C8 · UniProt A0A1D8NG21 · UniProt A0A1D8NDL1 · UniProt A0A371C2D0 · UniProt A0A1H6PPE5 · UniProt A0A1D8NKB4 · UniProt A0A1D8N7X0 · UniProt A0A1D8N3H5 · UniProt A0A1D8ND94 · UniProt A0A1D8NGI5 · UniProt A0A371C0F2 · UniProt A0A1D8N596 · UniProt A0A1D8NFX6 · UniProt A0A1H6PJS3 · UniProt A0A1D8N5V2 · UniProt A0A1H6Q311 · UniProt A0A371CFV9 · UniProt A0A1H6PKH9 · UniProt A0A1D8NNZ0