SMTL ID : 7sq9.1

Cryo-EM structure of mouse temsirolimus/PI(3,5)P2-bound TRPML1 channel at 2.11 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 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: 15 residues within 4Å: Chain A: Y.47, K.55, K.59, R.61, K.62, C.64, K.65, L.311, L.314, L.315, R.318, S.319, R.322, Y.355, R.403 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:L.311, A:L.315 Hydrogen bonds: A:Y.47, A:K.55, A:C.64, A:K.65, A:R.318, A:S.319, A:S.319, A:R.322, A:Y.355 Salt bridges: A:K.55, A:K.59, A:R.61, A:K.65, A:K.65, A:R.318, A:R.318, A:R.322, A:R.403 EUJ.9: 15 residues within 4Å: Chain B: Y.47, K.55, K.59, R.61, K.62, C.64, K.65, L.311, L.314, L.315, R.318, S.319, R.322, Y.355, R.403 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:L.311, B:L.315 Hydrogen bonds: B:Y.47, B:K.55, B:C.64, B:K.65, B:R.318, B:S.319, B:S.319, B:R.322, B:Y.355 Salt bridges: B:K.55, B:K.59, B:R.61, B:K.65, B:K.65, B:R.318, B:R.318, B:R.322, B:R.403 EUJ.11: 15 residues within 4Å: Chain C: Y.47, K.55, K.59, R.61, K.62, C.64, K.65, L.311, L.314, L.315, R.318, S.319, R.322, Y.355, R.403 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:L.311, C:L.315 Hydrogen bonds: C:Y.47, C:K.55, C:C.64, C:K.65, C:R.318, C:S.319, C:S.319, C:R.322, C:Y.355 Salt bridges: C:K.55, C:K.59, C:R.61, C:K.65, C:K.65, C:R.318, C:R.318, C:R.322, C:R.403 EUJ.13: 15 residues within 4Å: Chain D: Y.47, K.55, K.59, R.61, K.62, C.64, K.65, L.311, L.314, L.315, R.318, S.319, R.322, Y.355, R.403 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:L.311, D:L.315 Hydrogen bonds: D:Y.47, D:K.55, D:C.64, D:K.65, D:R.318, D:S.319, D:S.319, D:R.322, D:Y.355 Salt bridges: D:K.55, D:K.59, D:R.61, D:K.65, D:K.65, D:R.318, D:R.318, D:R.322, D:R.403

4 x A4I: (1R,2R,4S)-4-{(2R)-2-[(3S,6R,7E,9R,10R,12R,14S,15E,17E,19E,21S,23S,26R,27R,30S,34aS)-9,27-dihydroxy-10,21-dimethoxy-6,8,12,14,20,26-hexamethyl-1,5,11,28,29-pentaoxo-1,4,5,6,9,10,11,12,13,14,21,22,23,24,25,26,27,28,29,31,32,33,34,34a-tetracosahydro-3H-23,27-epoxypyrido[2,1-c][1,4]oxazacyclohentriacontin-3-yl]propyl}-2-methoxycyclohexyl 3-hydroxy-2-(hydroxymethyl)-2-methylpropanoate(Non-covalent)

A4I.6: 17 residues within 4Å: Chain A: L.422, V.425, M.426, C.429, V.432, A.433, Y.436, L.437, S.461, F.465, F.513 Chain C: Y.499, S.500, S.503, L.504, Y.507, M.508 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:L.422, A:V.425, A:Y.436, A:F.513, C:Y.499, C:Y.499, C:Y.507 Hydrogen bonds: A:S.461, C:S.500 A4I.10: 17 residues within 4Å: Chain B: L.422, V.425, M.426, C.429, V.432, A.433, Y.436, L.437, S.461, F.465, F.513 Chain D: Y.499, S.500, S.503, L.504, Y.507, M.508 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:L.422, B:V.425, B:Y.436, B:F.513, D:Y.499, D:Y.499, D:Y.507 Hydrogen bonds: B:S.461, D:S.500 A4I.12: 17 residues within 4Å: Chain B: Y.499, S.500, S.503, L.504, Y.507, M.508 Chain C: L.422, V.425, M.426, C.429, V.432, A.433, Y.436, L.437, S.461, F.465, F.513 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:L.422, C:V.425, C:Y.436, C:F.513, B:Y.499, B:Y.499, B:Y.507 Hydrogen bonds: C:S.461, B:S.500 A4I.14: 17 residues within 4Å: Chain A: Y.499, S.500, S.503, L.504, Y.507, M.508 Chain D: L.422, V.425, M.426, C.429, V.432, A.433, Y.436, L.437, S.461, F.465, F.513 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:Y.499, A:Y.499, A:Y.507, D:L.422, D:V.425, D:Y.436, D:F.513 Hydrogen bonds: A:S.500, D:S.461

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

NA.7: 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.8: 0 residues within 4Å: (No contacts) 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 2 interactions with chain C Water bridges: A:G.470, A:G.470, D:G.470, C:G.470, C: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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