SMTL ID : 7sq6.1

Cryo-EM structure of mouse agonist ML-SA1-bound TRPML1 channel at 2.32 Angstrom resolution

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 7 residues within 4Å: Chain A: R.168, V.188, I.229, N.230, T.232, T.261, R.274 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.188 NAG-NAG.2: 7 residues within 4Å: Chain B: R.168, V.188, I.229, N.230, T.232, T.261, R.274 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.188 NAG-NAG.3: 7 residues within 4Å: Chain C: R.168, V.188, I.229, N.230, T.232, T.261, R.274 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.188 NAG-NAG.4: 7 residues within 4Å: Chain D: R.168, V.188, I.229, N.230, T.232, T.261, R.274 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.188

4 x AQV: 2-{2-oxo-2-[(4S)-2,2,4-trimethyl-3,4-dihydroquinolin-1(2H)-yl]ethyl}-1H-isoindole-1,3(2H)-dione(Non-covalent)

AQV.5: 14 residues within 4Å: Chain A: F.428, C.429, V.432, A.433, Y.436, S.461, F.465, I.468, F.505, V.509, L.510, F.513 Chain D: Y.499, Y.507 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:Y.436, A:F.465, A:F.465, A:L.510, A:F.513, D:Y.499, D:Y.507 pi-Stacking: A:Y.436 AQV.7: 14 residues within 4Å: Chain A: Y.499, Y.507 Chain B: F.428, C.429, V.432, A.433, Y.436, S.461, F.465, I.468, F.505, V.509, L.510, F.513 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.499, A:Y.507, B:Y.436, B:F.465, B:F.465, B:L.510, B:F.513 pi-Stacking: B:Y.436 AQV.8: 14 residues within 4Å: Chain B: Y.499, Y.507 Chain C: F.428, C.429, V.432, A.433, Y.436, S.461, F.465, I.468, F.505, V.509, L.510, F.513 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:Y.499, B:Y.507, C:Y.436, C:F.465, C:F.465, C:L.510, C:F.513 pi-Stacking: C:Y.436 AQV.10: 14 residues within 4Å: Chain C: Y.499, Y.507 Chain D: F.428, C.429, V.432, A.433, Y.436, S.461, F.465, I.468, F.505, V.509, L.510, F.513 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.436, D:F.465, D:F.465, D:L.510, D:F.513, C:Y.499, C:Y.507 pi-Stacking: D:Y.436

2 x NA: SODIUM ION(Non-functional Binders)

NA.6: 4 residues within 4Å: Chain A: D.471 Chain B: D.471 Chain C: D.471 Chain D: D.471 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.471 NA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gan, N. et al., Structural mechanism of allosteric activation of TRPML1 by PI(3,5)P 2 and rapamycin. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-02-02

Peptides

Mucolipin-1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Mucolipin-1

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