Cryo-EM structure of human respiratory complex I

Structure

electron microscopy · 44 distinct chains · 51% helix, 5% strand (DSSP).

Ligands and binding sites

• PLX · (9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2lambda~5~-aza-6lambda~5~-phosphaoctacosane-6,6,11-triol · ligand · 9 copies · chains B, Q, U, W, s, j, V, l, o, a, b, d, e, r, g, h, i, f
• SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B, C, Q, M
• CDL · Cardiolipin · ligand · 5 copies · chains V, i, l, g, r, w, a, c, o, n, u
• PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 4 copies · chains V, i, r, S, W, j, m, s, Q, l, c
• 8Q1 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate · ligand · 2 copies · chains E, G, X, p
• FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains M, O
• FMN · Flavin mononucleotide · ligand · chains A
• NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains J

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

202 interfaces between chains.

• A–O · 3113 Ų buried · 32 hydrogen bonds · protein-protein
• k–m · 3003 Ų buried · 15 hydrogen bonds · protein-protein
• j–s · 2764 Ų buried · 11 hydrogen bonds · protein-protein
• P–Q · 2547 Ų buried · 22 hydrogen bonds · protein-protein
• l–r · 2188 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

• 5XTD · Cryo-EM structure of human respiratory complex I · the same entry in another collection · chain L against L, 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 5XTD · PDBe 5XTD · UniProt P49821 · UniProt O00217 · UniProt O75251 · UniProt P56556 · UniProt O43678 · UniProt O14561 · UniProt Q16718 · UniProt O95182 · UniProt Q16795 · UniProt P56181 · UniProt O43181 · UniProt P28331 · UniProt Q9UI09 · UniProt P19404 · UniProt O75489 · UniProt O75306 · UniProt O15239 · UniProt O75380 · UniProt O95167 · UniProt Q86Y39 · UniProt Q9P0J0 · UniProt O95178 · UniProt O43676 · UniProt O43674 · UniProt O95139 · UniProt O95169 · UniProt O96000 · UniProt Q9NX14 · UniProt O43677 · UniProt O95298 · UniProt O43920 · UniProt Q4GRX1 · UniProt B9EE38 · UniProt V9JN72 · UniProt X5BVZ3 · UniProt Q8HAX7 · UniProt O75438 · UniProt O95168 · UniProt Q9Y6M9 · UniProt B2XJG5 · UniProt H9PGF0 · UniProt P51970 · UniProt P17568 · UniProt O95299