Cryo-EM structure of the hexameric plasma membrane H+-ATPase in the active state (pH 6.0, BEF3-, conformation 1, C1 symmetry)

Structure

electron microscopy · 1 distinct chain · 52% helix, 15% strand (DSSP).

Ligands and binding sites

• POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 57 copies · chains A, B, F, C, D, E
• BEF · Beryllium trifluoride ion · ligand · 6 copies · chains A, B, C, D, E, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• C–D · 700 Ų buried · 6 hydrogen bonds · protein-protein
• E–F · 698 Ų buried · 6 hydrogen bonds · protein-protein
• B–C · 693 Ų buried · 5 hydrogen bonds · protein-protein
• A–F · 686 Ų buried · 6 hydrogen bonds · protein-protein
• A–B · 681 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 covalent (covalent ligand).

Compared structures

• 7VH6 · Cryo-EM structure of the hexameric plasma membrane H+-ATPase in the active state (pH 6.0… · the same entry in another collection · chain C against C, TM-score 1.00
• P05030 · AlphaFold monomer V2.0 prediction for plasma membrane ATPase 1 (P05030) · a predicted model of the same protein · chain A against A, TM-score 0.78

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 P05030
• Elsewhere: RCSB PDB 7VH6 · PDBe 7VH6 · UniProt P05030