Cryo-EM structure of a respiratory complex I assembly intermediate with NDUFAF2

Structure

electron microscopy · 41 distinct chains · 49% helix, 7% strand (DSSP).

Ligands and binding sites

• 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 10 copies · chains C, I, W, g, 1, J, 4, 2, 5, 3, b, i, a, D, 6
• SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, C, B, I, K
• CDL · Cardiolipin · ligand · 4 copies · chains J, j, 2, 5, X, g, 1, 3, 6, S, i, n, 4
• PLC · Diundecyl phosphatidyl choline · ligand · 4 copies · chains C, I, W, 1, U, g, S, i, n, 4, 5, R
• T7X · Phosphatidylinositol · ligand · 3 copies · chains X, b, 2, L, 5, 6, C, 4
• FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, H
• LMN · Lauryl Maltose Neopentyl Glycol · ligand · 2 copies · chains J, 2, 4, a, j
• 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
• NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains E
• CPL · 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine · ligand · chains b, 2

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

180 interfaces between chains.

• B–H · 3354 Ų buried · 33 hydrogen bonds · protein-protein
• L–6 · 2879 Ų buried · 7 hydrogen bonds · protein-protein
• 1–3 · 2857 Ų buried · 10 hydrogen bonds · protein-protein
• A–Y · 2551 Ų buried · 24 hydrogen bonds · protein-protein
• 4–5 · 2419 Ų buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

• 6RFQ · Cryo-EM structure of a respiratory complex I assembly intermediate with NDUFAF2 · the same entry in another collection · chain C against C, 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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• Every structure of UniProt A0A1D8NC63
• Every structure of UniProt A0A371BY45
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• Every structure of UniProt Q6ZY23
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• Elsewhere: RCSB PDB 6RFQ · PDBe 6RFQ · UniProt Q9UUU3 · UniProt Q9UUU2 · UniProt Q9UUU1 · UniProt A0A1D8NC63 · UniProt A0A371BY45 · UniProt A0A371C5F3 · UniProt Q9UUU0 · UniProt Q9UUT9 · UniProt Q9UUT8 · UniProt A0A371CB65 · UniProt Q9UUT7 · UniProt Q9B6D4 · UniProt A0A1H6PXT9 · UniProt A0A1D8N3C8 · UniProt A0A1D8NG21 · UniProt A0A1D8NDL1 · UniProt Q6ZY23 · UniProt A0A371C2D0 · UniProt A0A1H6PPE5 · UniProt A0A1D8NKB4 · UniProt A0A1D8N7X0 · UniProt A0A1D8N3H5 · UniProt A0A1D8ND94 · UniProt A0A1D8NGI5 · UniProt A0A371C0F2 · UniProt A0A1D8N596 · UniProt A0A1D8NFX6 · UniProt A0A1H6PJS3 · UniProt A0A1D8NJR0 · UniProt A0A1H6Q311 · UniProt Q6ZY24 · UniProt A0A1D8NGE3 · UniProt A0A371CFV9 · UniProt S5U3V2 · UniProt S5U4R9 · UniProt S5TMS4 · UniProt S5TMP9 · UniProt S5TF58 · UniProt Q9B6E9 · UniProt A0A1H6PKH9 · UniProt A0A1D8NNZ0