SMTL ID : 9j3z.1

Cryo-EM structure of lysosome cholesterol sencing protein in L state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

POV.1: 13 residues within 4Å: Chain A: L.47, L.54, I.58, R.61, A.62, I.388, V.389, I.392, S.393, W.396, F.708, L.713, K.715 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.47, A:L.54, A:I.58, A:I.58, A:I.388, A:V.389, A:V.389, A:I.392, A:W.396, A:W.396, A:W.396, A:W.396, A:F.708, A:F.708, A:L.713 Salt bridges: A:R.61, A:R.61, A:K.715 POV.2: 9 residues within 4Å: Chain A: V.124, A.125, F.137, S.274, V.278, L.281, L.282, T.284, A.285 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.124, A:A.125, A:F.137, A:F.137, A:V.278, A:L.281, A:L.282, A:T.284, A:A.285 Salt bridges: A:K.133 POV.4: 13 residues within 4Å: Chain B: L.47, L.54, I.58, R.61, A.62, I.388, V.389, I.392, S.393, W.396, F.708, L.713, H.716 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.47, B:L.54, B:L.54, B:V.389, B:W.396, B:W.396, B:L.713 Salt bridges: B:R.61, B:R.61 POV.5: 10 residues within 4Å: Chain B: L.120, T.121, L.123, V.124, A.125, K.133, F.137, V.278, L.281, A.285 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.120, B:T.121, B:V.124, B:A.125, B:K.133, B:F.137, B:V.278, 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.3: 3 residues within 4Å: Chain A: Y.162, S.306, N.309 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.306, A:N.309 NAG.6: 3 residues within 4Å: Chain B: D.305, S.306, N.309 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.305, 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

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

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