Cryoem structure of a human gamma-aminobutyric acid receptor, the GABA(A)R-BETA3 homopentamer, in complex with histamine and megabody MB25 in lipid nanodisc

Structure

electron microscopy · 2 distinct chains · 30% helix, 37% strand (DSSP).

Ligands and binding sites

• D10 · Decane · ligand · 4 copies · chains A
• R16 · Hexadecane · ligand · chains A
• HSM · Histamine · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, O
• MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, O
• BMA · beta-D-mannopyranose · sugar · chains A
• CL · Chloride ion · ion · 2 copies · chains A
• OCT · N-octane · additive · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–O · 567 Ų buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 glycan, 2 disulfide (N-glycosylation, disulfide).

Compared structures

• 7A5V · CryoEM structure of a human gamma-aminobutyric acid receptor, the GABA(A)R-beta3… · the same entry in another collection · chain A against A, TM-score 1.00
• P28472 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit beta-3… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P28472
• Elsewhere: RCSB PDB 7A5V · PDBe 7A5V · UniProt P28472