9J3X | pdb_00009j3x

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

PDB DOI: https://doi.org/10.2210/pdb9J3X/pdb
EM Map EMD-61127: EMDB EMDataResource

Classification: LIPID BINDING PROTEIN
Organism(s): Homo sapiens, Nomascus leucogenys
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-08-08 Released: 2025-04-02
Deposition Author(s): Qian, H.W., Wang, Z.H.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural basis for cholesterol sensing of LYCHOS and its interaction with indoxyl sulfate

Wang, Z., He, J., Yang, Y., He, Y., Qian, H.

(2025) Nat Commun 16: 2815

DOI: https://doi.org/10.1038/s41467-025-58087-9

Macromolecule Content

Total Structure Weight: 199.86 kDa
Atom Count: 8,894
Modelled Residue Count: 1,156
Deposited Residue Count: 1,740
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimera of Lysosomal cholesterol signaling protein and G protein-coupled receptor 155	A, B	870	Homo sapiens, Nomascus leucogenys This entity is chimeric	Mutation(s): 0 Gene Names: GPR155, PGR22
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z3F1 (Homo sapiens) Explore Q7Z3F1 Go to UniProtKB: Q7Z3F1
PHAROS: Q7Z3F1 GTEx: ENSG00000163328
Find proteins for G1R1S1 (Nomascus leucogenys) Explore G1R1S1 Go to UniProtKB: G1R1S1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	G1R1S1Q7Z3F1
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q7Z3F1-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV (Subject of Investigation/LOI) Query on POV Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	D [auth A] E [auth A] F [auth A] I [auth B] J [auth B] D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
CLR (Subject of Investigation/LOI) Query on CLR Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]