SMTL ID : 6e7z.1

cryo-EM structure of human TRPML1 with ML-SA1 and PI35P2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.73 Å

Oligo State

homo-tetramer

Ligands

4 x HZ7: (1R,2S,3S,4R,5S,6R)-5-{[(R)-[(2R)-2,3-bis{[(1S)-1-hydroxyoctyl]oxy}propoxy](hydroxy)phosphoryl]oxy}-2,4,6-trihydroxycyclohexane-1,3-diyl bis[dihydrogen (phosphate)](Non-covalent)

HZ7.1: 8 residues within 4Å: Chain A: K.55, R.61, K.65, R.318, S.319, R.322, L.325, Y.355 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.325 Hydrogen bonds: A:Y.355, A:Y.355, A:Y.355 Salt bridges: A:K.55, A:R.61, A:K.65, A:R.318, A:R.318, A:R.322 HZ7.3: 8 residues within 4Å: Chain B: K.55, R.61, K.65, R.318, S.319, R.322, L.325, Y.355 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.325 Hydrogen bonds: B:Y.355, B:Y.355, B:Y.355 Salt bridges: B:K.55, B:R.61, B:K.65, B:R.318, B:R.318, B:R.322 HZ7.5: 8 residues within 4Å: Chain C: K.55, R.61, K.65, R.318, S.319, R.322, L.325, Y.355 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.325 Hydrogen bonds: C:Y.355, C:Y.355, C:Y.355 Salt bridges: C:K.55, C:R.61, C:K.65, C:R.318, C:R.318, C:R.322 HZ7.7: 8 residues within 4Å: Chain D: K.55, R.61, K.65, R.318, S.319, R.322, L.325, Y.355 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.325 Hydrogen bonds: D:Y.355, D:Y.355, D:Y.355 Salt bridges: D:K.55, D:R.61, D:K.65, D:R.318, D:R.318, D:R.322

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(Covalent)

AQV.2: 7 residues within 4Å: Chain A: C.429, A.433, Y.436, F.465, I.468, F.513 Chain D: Y.507 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:A.433, A:Y.436, A:F.513, D:Y.507, D:Y.507 Hydrogen bonds: A:Y.436 AQV.4: 7 residues within 4Å: Chain A: Y.507 Chain B: C.429, A.433, Y.436, F.465, I.468, F.513 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.433, B:Y.436, B:F.513, A:Y.507, A:Y.507 Hydrogen bonds: B:Y.436 AQV.6: 7 residues within 4Å: Chain B: Y.507 Chain C: C.429, A.433, Y.436, F.465, I.468, F.513 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:A.433, C:Y.436, C:F.513, B:Y.507, B:Y.507 Hydrogen bonds: C:Y.436 AQV.8: 7 residues within 4Å: Chain C: Y.507 Chain D: C.429, A.433, Y.436, F.465, I.468, F.513 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:A.433, D:Y.436, D:F.513, C:Y.507, C:Y.507 Hydrogen bonds: D:Y.436

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fine, M. et al., Structural basis for PtdInsP2-mediated human TRPML1 regulation. Nat Commun (2018)

Release Date

2018-11-28

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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