SMTL ID : 8z8z.1

Cryo-EM structure of LYCHOS

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: Y.165, E.167, N.312 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.164, A:N.312 NAG.10: 3 residues within 4Å: Chain B: Y.165, E.167, N.312 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.164, B:N.312

6 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)

6OU.2: 9 residues within 4Å: Chain A: I.61, R.64, V.392, I.395, S.396, W.399, F.711 Ligands: 01.6, LBN.9 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.61, A:V.392, A:I.395, A:S.396, A:W.399, A:W.399, A:W.399, A:W.399, A:F.711, A:F.711, A:F.711 Salt bridges: A:R.64, A:R.64 6OU.3: 14 residues within 4Å: Chain A: V.120, L.123, T.124, V.127, A.128, S.129, K.136, F.140, V.281, L.284, L.285, T.287, A.288, V.292 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.120, A:V.120, A:L.123, A:T.124, A:V.127, A:F.140, A:F.140, A:L.284, A:L.284, A:L.285, A:A.288, A:V.292 Hydrogen bonds: A:S.129, A:S.129 6OU.4: 10 residues within 4Å: Chain A: R.298, F.321, V.363, S.364, L.367, A.674, L.695, F.698 Ligands: CLR.5, 01.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.321, A:V.363, A:L.367, A:A.674, A:F.698, A:F.698, A:F.698 Salt bridges: A:R.298, A:R.298 6OU.11: 9 residues within 4Å: Chain B: I.61, R.64, V.392, I.395, S.396, W.399, F.711 Ligands: LBN.7, 01.15 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.61, B:V.392, B:I.395, B:S.396, B:W.399, B:W.399, B:W.399, B:W.399, B:F.711, B:F.711, B:F.711 Salt bridges: B:R.64, B:R.64 6OU.12: 14 residues within 4Å: Chain B: V.120, L.123, T.124, V.127, A.128, S.129, K.136, F.140, V.281, L.284, L.285, T.287, A.288, V.292 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.120, B:V.120, B:L.123, B:T.124, B:V.127, B:F.140, B:F.140, B:L.284, B:L.284, B:L.285, B:A.288, B:V.292 Hydrogen bonds: B:S.129, B:S.129 6OU.13: 10 residues within 4Å: Chain B: R.298, F.321, V.363, S.364, L.367, A.674, L.695, F.698 Ligands: CLR.14, 01.15 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.321, B:V.363, B:L.367, B:A.674, B:F.698, B:F.698, B:F.698 Salt bridges: B:R.298, B:R.298

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.5: 12 residues within 4Å: Chain A: F.279, I.283, I.286, T.287, L.290, L.291, I.352, V.356, I.360, L.663 Ligands: 6OU.4, 01.6 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.279, A:I.286, A:I.286, A:T.287, A:L.290, A:L.291, A:L.291, A:I.352, A:V.356, A:V.356, A:L.663 CLR.14: 12 residues within 4Å: Chain B: F.279, I.283, I.286, T.287, L.290, L.291, I.352, V.356, I.360, L.663 Ligands: 6OU.13, 01.15 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.279, B:I.286, B:I.286, B:T.287, B:L.290, B:L.291, B:L.291, B:I.352, B:V.356, B:V.356, B:L.663

2 x 01: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (4~{Z},7~{Z},10~{Z},13~{Z},16~{Z},19~{Z})-docosa-4,7,10,13,16,19-hexaenoate

01.6: 25 residues within 4Å: Chain A: L.49, F.53, L.57, Y.60, M.267, G.269, K.270, I.271, V.351, F.355, P.359, I.360, Y.362, I.389, R.660, G.705, F.708, I.709, G.712, I.713, L.716, D.717 Ligands: 6OU.2, 6OU.4, CLR.5 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:L.49, A:F.53, A:L.57, A:Y.60, A:F.355, A:F.355, A:F.355, A:F.355, A:P.359, A:I.360, A:Y.362, A:I.389, A:F.708, A:F.708, A:I.713 Hydrogen bonds: A:Y.60, A:G.269, A:K.270, A:I.271, A:R.660, A:D.717, A:D.717 01.15: 25 residues within 4Å: Chain B: L.49, F.53, L.57, Y.60, M.267, G.269, K.270, I.271, V.351, F.355, P.359, I.360, Y.362, I.389, R.660, G.705, F.708, I.709, G.712, I.713, L.716, D.717 Ligands: 6OU.11, 6OU.13, CLR.14 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:L.49, B:F.53, B:L.57, B:Y.60, B:F.355, B:F.355, B:F.355, B:F.355, B:P.359, B:I.360, B:Y.362, B:I.389, B:F.708, B:F.708, B:I.713 Hydrogen bonds: B:Y.60, B:G.269, B:K.270, B:I.271, B:R.660, B:D.717, B:D.717

2 x LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine(Non-covalent)

LBN.7: 18 residues within 4Å: Chain A: R.82, F.83, P.86, A.87, F.90, M.225, F.232, V.244, F.247, L.248, L.251 Chain B: G.54, L.57, C.58, I.61, A.65, V.67 Ligands: 6OU.11 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.83, A:F.90, A:F.232, A:V.244, A:F.247, A:F.247, A:L.248, A:L.251, B:L.57, B:I.61 Salt bridges: A:R.82 LBN.9: 18 residues within 4Å: Chain A: G.54, L.57, C.58, I.61, A.65, V.67 Chain B: R.82, F.83, P.86, A.87, F.90, M.225, F.232, V.244, F.247, L.248, L.251 Ligands: 6OU.2 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.83, B:F.90, B:F.232, B:V.244, B:F.247, B:F.247, B:L.248, B:L.251, A:L.57, A:I.61 Salt bridges: B:R.82

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

NA.8: 4 residues within 4Å: Chain A: N.148, P.327, V.328, T.354 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.354 NA.16: 4 residues within 4Å: Chain B: N.148, P.327, V.328, T.354 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.328

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, Q. et al., Molecular architecture of human LYCHOS involved in lysosomal cholesterol signaling. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-01-01

Peptides

Lysosomal cholesterol signaling protein,Fluorescent 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,Fluorescent Protein