SMTL ID : 9j40.1

Cryo-EM structure of lysosome cholesterol sencing protein complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

6 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.1: 6 residues within 4Å: Chain A: I.58, R.61, I.392, W.396, F.708, L.713 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.58, A:I.392, A:W.396, A:W.396, A:F.708, A:L.713 Salt bridges: A:R.61, A:R.61 POV.4: 18 residues within 4Å: Chain A: F.43, L.46, V.53, Y.57, M.264, G.266, K.267, I.268, F.352, V.353, P.356, V.389, R.657, F.705, G.709, L.713, D.714 Ligands: CLR.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.43, A:V.53, A:Y.57, A:F.352, A:F.352, A:V.353, A:P.356, A:V.389, A:F.705, A:L.713 Hydrogen bonds: A:G.266, A:K.267, A:I.268 Salt bridges: A:D.714 POV.5: 9 residues within 4Å: Chain A: L.120, T.121, V.124, S.126, F.137, S.274, V.278, L.281, T.284 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.120, A:T.121, A:F.137, A:F.137, A:V.278, A:L.281, A:T.284 Hydrogen bonds: A:S.126, A:S.274 POV.8: 5 residues within 4Å: Chain B: I.58, R.61, W.396, F.708, L.713 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.58, B:W.396, B:W.396, B:F.708, B:L.713 Salt bridges: B:R.61, B:R.61 POV.11: 17 residues within 4Å: Chain B: F.43, L.46, F.50, V.53, Y.57, M.264, G.266, K.267, I.268, F.352, P.356, R.657, F.705, G.709, L.713, D.714 Ligands: CLR.10 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.43, B:F.50, B:V.53, B:Y.57, B:F.352, B:F.352, B:F.352, B:P.356, B:F.705, B:L.713 Hydrogen bonds: B:G.266, B:K.267, B:I.268 Salt bridges: B:D.714 POV.12: 9 residues within 4Å: Chain B: L.120, T.121, V.124, S.126, F.137, V.278, L.281, T.284, A.285 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.120, B:T.121, B:F.137, B:F.137, B:V.278, B:L.281, B:L.281, B:T.284 Hydrogen bonds: B:S.274

2 x IOS: 3-SULFOOXY-1H-INDOLE(Non-covalent)

IOS.2: 9 residues within 4Å: Chain A: S.78, L.82, N.145, F.147, A.256, Y.259, A.326, P.327, G.328 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.256, A:Y.259, A:P.327 Hydrogen bonds: A:S.78, A:N.145, A:G.328 IOS.9: 8 residues within 4Å: Chain B: S.78, L.82, N.145, F.147, A.256, A.326, P.327, G.328 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.256, B:P.327 Hydrogen bonds: B:S.78, B:G.328

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 7 residues within 4Å: Chain A: F.276, I.280, I.283, L.288, I.349, I.357 Ligands: POV.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.276, A:I.280, A:I.283, A:L.288, A:I.349, A:I.357 CLR.10: 7 residues within 4Å: Chain B: F.276, I.280, I.283, L.288, I.349, I.357 Ligands: POV.11 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.276, B:I.280, B:I.283, B:L.288, B:I.349, B:I.349, B:I.357

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 3 residues within 4Å: Chain A: Y.162, S.306, N.309 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.306, A:N.309, A:N.309 NAG.13: 4 residues within 4Å: Chain B: Y.162, E.164, S.306, N.309 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.306, B:N.309, B:N.309

2 x TRP: TRYPTOPHAN(Non-covalent)

TRP.7: 5 residues within 4Å: Chain A: R.270, K.273, F.276, T.656, L.660 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.270, A:T.656 Salt bridges: A:R.270 TRP.14: 5 residues within 4Å: Chain B: R.270, K.273, F.276, T.656, L.660 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.270, B:T.656 Salt bridges: B:R.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Z. et al., Structural basis for cholesterol sensing of LYCHOS and its interaction with indoxyl sulfate. Nat Commun (2025)

Release Date

2025-04-02

Peptides

G protein-coupled receptor 155,Lysosomal cholesterol signaling protein fusion protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Membrane

We predict this structure to be a membrane protein.
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G protein-coupled receptor 155,Lysosomal cholesterol signaling protein fusion protein

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