SMTL ID : 7sq7.1

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

Coordinates

PDB Format Compare

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 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(Non-covalent)

EUJ.5: 13 residues within 4Å: Chain A: Y.47, K.55, K.59, R.61, C.64, K.65, L.311, L.314, L.315, R.318, S.319, R.322, Y.355 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.311, A:L.315 Hydrogen bonds: A:K.55, A:C.64, A:K.65, A:R.318, A:R.318, A:S.319, A:S.319, A:Y.355 Salt bridges: A:K.55, A:K.55, A:K.59, A:R.61, A:K.62, A:K.65, A:K.65, A:R.318, A:R.322 EUJ.7: 13 residues within 4Å: Chain B: Y.47, K.55, K.59, R.61, C.64, K.65, L.311, L.314, L.315, R.318, S.319, R.322, Y.355 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:L.311, B:L.315 Hydrogen bonds: B:K.55, B:C.64, B:K.65, B:R.318, B:R.318, B:S.319, B:S.319, B:Y.355 Salt bridges: B:K.55, B:K.55, B:K.59, B:R.61, B:K.62, B:K.65, B:K.65, B:R.318, B:R.322 EUJ.8: 13 residues within 4Å: Chain C: Y.47, K.55, K.59, R.61, C.64, K.65, L.311, L.314, L.315, R.318, S.319, R.322, Y.355 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:L.311, C:L.315 Hydrogen bonds: C:K.55, C:C.64, C:K.65, C:R.318, C:R.318, C:S.319, C:S.319, C:Y.355 Salt bridges: C:K.55, C:K.55, C:K.59, C:R.61, C:K.62, C:K.65, C:K.65, C:R.318, C:R.322 EUJ.9: 13 residues within 4Å: Chain D: Y.47, K.55, K.59, R.61, C.64, K.65, L.311, L.314, L.315, R.318, S.319, R.322, Y.355 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:L.311, D:L.315 Hydrogen bonds: D:K.55, D:C.64, D:K.65, D:R.318, D:R.318, D:S.319, D:S.319, D:Y.355 Salt bridges: D:K.55, D:K.55, D:K.59, D:R.61, D:K.62, D:K.65, D:K.65, D:R.318, D:R.322

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

NA.6: 4 residues within 4Å: Chain A: G.470 Chain B: G.470 Chain C: G.470 Chain D: G.470 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.470

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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