SMTL ID : 9j3x.1

Cryo-EM structure of lysosome cholesterol sencing protein LYCHOS in Tight-state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 12 residues within 4Å: Chain A: R.270, L.271, F.276, I.280, I.283, T.284, L.287, I.349, V.353, I.357, L.660 Ligands: POV.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.271, A:F.276, A:F.276, A:I.280, A:I.283, A:L.287, A:I.349, A:I.349, A:V.353, A:I.357, A:L.660 Hydrogen bonds: A:R.270 CLR.6: 12 residues within 4Å: Chain B: R.270, L.271, F.276, I.280, I.283, T.284, L.287, I.349, V.353, I.357, L.660 Ligands: POV.7 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.271, B:F.276, B:F.276, B:I.280, B:I.283, B:L.287, B:I.349, B:I.349, B:V.353, B:I.357, B:L.660 Hydrogen bonds: B:R.270

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

POV.2: 30 residues within 4Å: Chain A: L.46, L.47, F.50, V.53, L.54, Y.57, M.264, G.266, K.267, I.268, R.270, V.348, F.352, V.353, A.355, P.356, V.360, V.389, R.657, F.695, F.699, F.705, I.706, G.709, I.710, L.713, D.714, K.715 Ligands: CLR.1, POV.3 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.46, A:L.47, A:F.50, A:F.50, A:V.53, A:L.54, A:F.352, A:F.352, A:V.353, A:P.356, A:V.360, A:V.389, A:F.695, A:F.699, A:F.705, A:I.706, A:I.710, A:L.713 Hydrogen bonds: A:Y.57, A:G.266, A:K.267, A:I.268 Salt bridges: A:D.714 POV.3: 15 residues within 4Å: Chain A: L.47, L.54, I.58, R.61, A.62, N.63, I.388, V.389, I.392, S.393, W.396, F.708, L.713, K.715 Ligands: POV.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.47, A:L.54, A:I.58, A:I.388, A:I.392, A:I.392, A:W.396, A:W.396, A:W.396, A:F.708, A:L.713 Hydrogen bonds: A:R.61 Salt bridges: A:R.61, A:K.715 POV.4: 10 residues within 4Å: Chain A: L.120, T.121, V.124, A.125, S.126, K.133, S.274, V.278, L.281, A.285 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.120, A:V.124, A:A.125, A:V.278, A:L.281, A:L.281, A:A.285 Salt bridges: A:K.133 POV.7: 30 residues within 4Å: Chain B: L.46, L.47, F.50, V.53, L.54, Y.57, M.264, G.266, K.267, I.268, R.270, V.348, F.352, V.353, A.355, P.356, V.360, V.389, R.657, F.695, F.699, F.705, I.706, G.709, I.710, L.713, D.714, K.715 Ligands: CLR.6, POV.8 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:L.46, B:L.47, B:F.50, B:F.50, B:V.53, B:L.54, B:F.352, B:F.352, B:V.353, B:P.356, B:V.360, B:V.389, B:F.695, B:F.699, B:F.705, B:I.706, B:I.710, B:L.713 Hydrogen bonds: B:Y.57, B:G.266, B:K.267, B:I.268 Salt bridges: B:D.714 POV.8: 15 residues within 4Å: Chain B: L.47, L.54, I.58, R.61, A.62, N.63, I.388, V.389, I.392, S.393, W.396, F.708, L.713, K.715 Ligands: POV.7 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.47, B:L.54, B:I.58, B:I.388, B:I.392, B:I.392, B:W.396, B:W.396, B:W.396, B:F.708, B:L.713 Hydrogen bonds: B:R.61 Salt bridges: B:R.61, B:K.715 POV.9: 10 residues within 4Å: Chain B: L.120, T.121, V.124, A.125, S.126, K.133, S.274, V.278, L.281, A.285 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.120, B:V.124, B:A.125, B:V.278, B:L.281, B:L.281, B:A.285 Salt bridges: B:K.133

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

NAG.5: 4 residues within 4Å: Chain A: Y.162, E.164, S.306, N.309 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.306, A:S.306, A:N.309, A:N.309 NAG.10: 4 residues within 4Å: Chain B: Y.162, E.164, S.306, N.309 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.306, B:S.306, B:N.309, B:N.309

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

Chimera of Lysosomal cholesterol signaling protein and G protein-coupled receptor 155: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Chimera of Lysosomal cholesterol signaling protein and G protein-coupled receptor 155