SMTL ID : 9cc2.1

Cryo-EM structure of mouse PI(4,5)P2-bound TRPML1 channel at 2.46 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: 6 residues within 4Å: Chain A: R.168, V.188, I.229, N.230, T.232, T.261 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.188 NAG-NAG.2: 6 residues within 4Å: Chain B: R.168, V.188, I.229, N.230, T.232, T.261 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.188 NAG-NAG.3: 6 residues within 4Å: Chain C: R.168, V.188, I.229, N.230, T.232, T.261 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.188 NAG-NAG.4: 6 residues within 4Å: Chain D: R.168, V.188, I.229, N.230, T.232, T.261 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.188

4 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-covalent)

PIO.5: 9 residues within 4Å: Chain A: Y.47, R.61, C.64, K.65, M.67, L.68, L.315, R.318, R.322 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:M.67, A:L.68 Hydrogen bonds: A:Y.47, A:K.65, A:K.65, A:R.322, A:R.322 Salt bridges: A:K.55, A:R.61, A:K.65, A:R.318 PIO.8: 9 residues within 4Å: Chain B: Y.47, R.61, C.64, K.65, M.67, L.68, L.315, R.318, R.322 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:M.67, B:L.68 Hydrogen bonds: B:Y.47, B:K.65, B:K.65, B:R.322, B:R.322 Salt bridges: B:K.55, B:R.61, B:K.65, B:R.318 PIO.10: 9 residues within 4Å: Chain C: Y.47, R.61, C.64, K.65, M.67, L.68, L.315, R.318, R.322 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:M.67, C:L.68 Hydrogen bonds: C:Y.47, C:K.65, C:K.65, C:R.322, C:R.322 Salt bridges: C:K.55, C:R.61, C:K.65, C:R.318 PIO.12: 9 residues within 4Å: Chain D: Y.47, R.61, C.64, K.65, M.67, L.68, L.315, R.318, R.322 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:M.67, D:L.68 Hydrogen bonds: D:Y.47, D:K.65, D:K.65, D:R.322, D:R.322 Salt bridges: D:K.55, D:R.61, D:K.65, D:R.318

4 x FO4: sphingomyelin(Non-covalent)

FO4.6: 21 residues within 4Å: Chain A: V.425, C.429, V.432, Y.436, S.456, L.457, S.458, S.461, F.465, I.468, F.513 Chain D: Q.481, Q.484, W.491, L.492, Q.495, L.496, Y.499, S.503, L.504, Y.507 20 PLIP interactions: 10 interactions with chain D, 10 interactions with chain A Hydrophobic interactions: D:W.491, D:L.492, D:Q.495, D:L.496, D:Y.499, D:Y.499, D:L.504, D:Y.507, D:Y.507, A:V.425, A:V.432, A:Y.436, A:Y.436, A:I.468, A:F.513, A:F.513 pi-Cation interactions: D:W.491 Hydrogen bonds: A:S.456, A:L.457, A:S.458 FO4.7: 21 residues within 4Å: Chain A: Q.481, Q.484, W.491, L.492, Q.495, L.496, Y.499, S.503, L.504, Y.507 Chain B: V.425, C.429, V.432, Y.436, S.456, L.457, S.458, S.461, F.465, I.468, F.513 19 PLIP interactions: 9 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:V.425, B:V.432, B:Y.436, B:Y.436, B:I.468, B:F.513, B:F.513, A:W.491, A:L.492, A:Q.495, A:L.496, A:Y.499, A:Y.499, A:L.504, A:Y.507, A:Y.507 Hydrogen bonds: B:S.456, B:S.458 pi-Cation interactions: A:W.491 FO4.9: 21 residues within 4Å: Chain B: Q.481, Q.484, W.491, L.492, Q.495, L.496, Y.499, S.503, L.504, Y.507 Chain C: V.425, C.429, V.432, Y.436, S.456, L.457, S.458, S.461, F.465, I.468, F.513 19 PLIP interactions: 10 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:W.491, B:L.492, B:Q.495, B:L.496, B:Y.499, B:Y.499, B:L.504, B:Y.507, B:Y.507, C:V.425, C:V.432, C:Y.436, C:Y.436, C:I.468, C:F.513, C:F.513 pi-Cation interactions: B:W.491 Hydrogen bonds: C:S.456, C:S.458 FO4.11: 21 residues within 4Å: Chain C: Q.481, Q.484, W.491, L.492, Q.495, L.496, Y.499, S.503, L.504, Y.507 Chain D: V.425, C.429, V.432, Y.436, S.456, L.457, S.458, S.461, F.465, I.468, F.513 19 PLIP interactions: 9 interactions with chain D, 10 interactions with chain C Hydrophobic interactions: D:V.425, D:V.432, D:Y.436, D:Y.436, D:I.468, D:F.513, D:F.513, C:W.491, C:L.492, C:Q.495, C:L.496, C:Y.499, C:Y.499, C:L.504, C:Y.507, C:Y.507 Hydrogen bonds: D:S.456, D:S.458 pi-Cation interactions: C:W.491

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gan, N. et al., TRPML1 gating modulation by allosteric mutations and lipids. Biorxiv (2024)

Release Date

2024-10-09

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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