Cryo-EM structure of mouse PI(3,5)P2-bound TRPML1 channel at 2.41 ångström resolution

Structure

electron microscopy · 1 distinct chain · 61% helix, 14% strand (DSSP).

Ligands and binding sites

• EUJ · (2R)-3-{[(S)-hydroxy{[(1s,2r,3r,4s,5s,6r)-2,4,6-trihydroxy-3,5-bis(phosphonooxy) cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate · ligand · 4 copies · chains A, B, C, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
• NA · Sodium ion · metal · chains A, B, C, D

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.

• A–B · 3508 Ų buried · 32 hydrogen bonds · protein-protein
• A–D · 3507 Ų buried · 31 hydrogen bonds · protein-protein
• B–C · 3500 Ų buried · 31 hydrogen bonds · protein-protein
• C–D · 3492 Ų buried · 31 hydrogen bonds · protein-protein
• B–D · 23 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 glycan (N-glycosylation).

Compared structures

• 7SQ7 · Cryo-EM structure of mouse PI(3,5)P2-bound TRPML1 channel at 2.41 Angstrom resolution · the same entry in another collection · chain A against A, TM-score 1.00
• Q99J21 · AlphaFold monomer V2.0 prediction for mucolipin-1 (Q99J21) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q99J21
• Elsewhere: RCSB PDB 7SQ7 · PDBe 7SQ7 · UniProt Q99J21