Cryo-EM structure of the human nax channel in complex with BETA3 solved in nanodiscs

Structure

electron microscopy · 2 distinct chains · 63% helix, 5% strand (DSSP).

Ligands and binding sites

• PLM · Palmitic acid · ligand · 6 copies · chains A
• PEV · (1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · 3 copies · chains A
• POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 3 copies · chains A
• CLR · Cholesterol · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1984 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 7TJ8 · Cryo-EM structure of the human Nax channel in complex with beta3 solved in nanodiscs · the same entry in another collection · chain A against A, TM-score 1.00
• Q01118 · AlphaFold monomer V2.0 prediction for sodium channel protein type 7 subunit alpha (Q01118) · a predicted model of the same protein · chain A against A, TM-score 0.97
• Q9NY72 · AlphaFold monomer V2.0 prediction for sodium channel subunit beta-3 (Q9NY72) · a predicted model of the same protein · chain B against A, TM-score 0.90

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 Q01118
• Every structure of UniProt Q9NY72
• Elsewhere: RCSB PDB 7TJ8 · PDBe 7TJ8 · UniProt Q01118 · UniProt Q9NY72