Cryo-EM structure of arabidopsis thaliana complex-I (closed conformation)

Structure

electron microscopy · 47 distinct chains · 47% helix, 8% strand (DSSP).

Ligands and binding sites

• SF4 · Iron/sulfur cluster · ligand · 6 copies · chains B, D, F, G, I
• PTY · Phosphatidylethanolamine · ligand · 3 copies · chains D, H, I, Z, b, M, g, N, d
• FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, G
• PC7 · (7S)-4-hydroxy-N,N,N-trimethyl-9-oxo-7-[(palmitoyloxy) methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide · ligand · 2 copies · chains L, M, c, N, f, v
• 8Q1 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate · ligand · 2 copies · chains U, W, L, T, n
• FMN · Flavin mononucleotide · ligand · chains F
• UQ9 · Ubiquinone-9 · ligand · chains B, H
• PGT · (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · chains N, f, y, z
• NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains P
• LMN · Lauryl Maltose Neopentyl Glycol · ligand · chains M, N, d
• PSF · 1,2-dicaproyl-sn-phosphatidyl-L-serine · ligand · chains N, d, x, z
• T7X · Phosphatidylinositol · ligand · chains f, v, y, z
• ZN · Zinc ion · metal · 2 copies · chains R, y, z
• FE · Fe (III) ion · metal · chains O

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

155 interfaces between chains.

• y–z · 2737 Ų buried · 30 hydrogen bonds · protein-protein
• x–z · 2682 Ų buried · 23 hydrogen bonds · protein-protein
• A–H · 2582 Ų buried · 2 hydrogen bonds · protein-protein
• x–y · 2542 Ų buried · 30 hydrogen bonds · protein-protein
• L–M · 2448 Ų buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 covalent, 3 disulfide (covalent ligand, disulfide).

Compared structures

• 7AR8 · Cryo-EM structure of Arabidopsis thaliana complex-I (closed conformation) · the same entry in another collection · chain N against N, 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
• Every structure of UniProt P92533
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• Every structure of UniProt A0A2P2CLH2
• Every structure of UniProt O22769
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• Elsewhere: RCSB PDB 7AR8 · PDBe 7AR8 · UniProt P92533 · UniProt Q42577 · UniProt Q95748 · UniProt A0A2P2CLH2 · UniProt O22769 · UniProt Q9FNN5 · UniProt Q9FGI6 · UniProt B5TM92 · UniProt Q42599 · UniProt A0A2P2CLG1 · UniProt A0A2P2CLH7 · UniProt B5TM94 · UniProt B5TM93 · UniProt O05000 · UniProt A0A384LA38 · UniProt Q9SK66 · UniProt Q9FJW4 · UniProt Q9M9M6 · UniProt Q9FIJ2 · UniProt P53665 · UniProt O80800 · UniProt Q9FLX7 · UniProt Q9LHI0 · UniProt Q8LGE7 · UniProt Q8RWA7 · UniProt Q9C9Z5 · UniProt Q9ZPY5 · UniProt Q8VZT9 · UniProt Q94AL6 · UniProt Q9LZI6 · UniProt Q84W12 · UniProt Q9SLC8 · UniProt A0A178W1I8 · UniProt Q8LDK3 · UniProt O64725 · UniProt Q9FGK0 · UniProt A0A178VZI4 · UniProt Q945M1 · UniProt Q9SKC9 · UniProt Q94C12 · UniProt Q9M9M9 · UniProt Q9SD78 · UniProt Q9ZUX4 · UniProt Q9SMN1 · UniProt Q9C6B3 · UniProt Q9FWR5