SMTL ID : 8y56.1

Cryo-EM reveals cholesterol binding in the lysosomal GPCR-like protein LYCHOS

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: T.146, Q.147, S.180, L.184 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.180

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 6 residues within 4Å: Chain A: R.65, I.396, W.400, F.709, F.712 Ligands: CLR.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.396, A:W.400, A:F.709, A:F.712, A:F.712 CLR.3: 11 residues within 4Å: Chain A: L.463, L.467, I.470, P.484, I.487, I.488, S.491, I.495, V.530, C.534, I.538 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.467, A:I.470, A:I.470, A:I.487, A:I.488, A:I.495, A:V.530, A:I.538 CLR.4: 10 residues within 4Å: Chain A: F.47, L.51, L.58, F.356, A.359, Y.363, D.389, I.390, F.709 Ligands: CLR.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.47, A:L.51, A:L.58, A:F.356, A:F.356, A:Y.363, A:Y.363, A:I.390, A:F.709 CLR.5: 13 residues within 4Å: Chain A: V.121, L.124, T.125, V.128, A.129, S.130, K.137, F.141, V.282, L.285, L.286, T.288, V.293 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.121, A:L.124, A:V.128, A:A.129, A:K.137, A:F.141, A:F.141, A:V.282, A:V.282, A:L.286, A:L.286, A:T.288 Hydrogen bonds: A:S.130 CLR.6: 7 residues within 4Å: Chain A: N.421, I.424, L.453, S.456, S.457, I.489, W.493 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.424, A:L.453, A:I.489, A:W.493, A:W.493

1 x DKB: [(2R)-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] octadecanoate(Non-covalent)

DKB.7: 17 residues within 4Å: Chain A: F.280, L.283, I.284, I.287, T.288, L.291, L.292, F.322, I.353, V.357, P.360, I.361, V.364, S.365, L.368, L.369, F.699 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.280, A:F.280, A:L.283, A:I.287, A:L.291, A:L.292, A:I.353, A:I.353, A:V.357, A:P.360, A:I.361, A:I.361, A:I.361 Hydrogen bonds: A:S.365

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, J. et al., Cryo-EM reveals cholesterol binding in the lysosomal GPCR-like protein LYCHOS. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-01-29

Peptides

Lysosomal cholesterol signaling protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

Membrane

We predict this structure to be a membrane protein.
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Lysosomal cholesterol signaling protein