8Z8Z | pdb_00008z8z

Cryo-EM structure of LYCHOS

PDB DOI: https://doi.org/10.2210/pdb8Z8Z/pdb
EM Map EMD-39851: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, synthetic construct
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes mpstruc

Deposited: 2024-04-22 Released: 2025-01-01
Deposition Author(s): Xiong, Q., Zhu, Z., Li, T., Zhou, Z., Chao, Y., Qu, Q., Li, D.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.11 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Molecular architecture of human LYCHOS involved in lysosomal cholesterol signaling.

Xiong, Q., Zhu, Z., Li, T., Li, X., Zhou, Z., Chao, Y., Yang, C., Feng, S., Qu, Q., Li, D.

(2025) Nat Struct Mol Biol 32: 905-913

PubMed: 39824977 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-024-01474-5
Primary Citation Related Structures:
8Z8Z

PubMed Abstract:
Lysosomal membrane protein LYCHOS (lysosomal cholesterol signaling) translates cholesterol abundance to mammalian target of rapamycin activation. Here we report the 2.11-Å structure of human LYCHOS, revealing a unique fusion architecture comprising a G-protein-coupled receptor (GPCR)-like domain and a transporter domain that mediates homodimer assembly. The NhaA-fold transporter harbors a previously uncharacterized intramembrane Na ⁺ pocket. The GPCR-like domain is stabilized, by analogy to canonical GPCRs, in an inactive state through 'tethered antagonism' by a lumenal loop and strong interactions at the cytosol side preventing the hallmark swing of the sixth transmembrane helix seen in active GPCRs. A cholesterol molecule and an associated docosahexaenoic acid (DHA)-phospholipid are entrapped between the transporter and GPCR-like domains, with the DHA-phospholipid occupying a pocket previously implicated in cholesterol sensing, indicating inter-domain coupling via dynamic lipid-protein interactions. Our work provides a high-resolution framework for functional investigations of the understudied LYCHOS protein.

Organizational Affiliation

The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.

Macromolecule Content

Total Structure Weight: 263.04 kDa
Atom Count: 9,410
Modeled Residue Count: 1,158
Deposited Residue Count: 2,288
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysosomal cholesterol signaling protein,Fluorescent Protein	A, B	1,144	Homo sapiens, synthetic construct This entity is chimeric	Mutation(s): 0 Gene Names: GPR155, PGR22 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z3F1 (Homo sapiens) Explore Q7Z3F1 Go to UniProtKB: Q7Z3F1
PHAROS: Q7Z3F1 GTEx: ENSG00000163328
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7Z3F1
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q7Z3F1-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L1C (Subject of Investigation/LOI) Query on A1L1C Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain Q [auth B] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth B]	H [auth A], Q [auth B]	[(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 C₄₃ H₇₄ N O₈ P MPWUZHVZZKSTPV-MADBQMNMSA-N		Interactions Focus chain H [auth A] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain Q [auth B]
LBN Query on LBN Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B]	I [auth A], K [auth B]	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-VYOBOKEXSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Interactions & Density Focus chain I [auth A] Focus chain K [auth B]
6OU Query on 6OU 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 M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	D [auth A] E [auth A] F [auth A] M [auth B] N [auth B] D [auth A], E [auth A], F [auth A], M [auth B], N [auth B], O [auth B]	[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate C₃₉ H₇₆ N O₈ P FHQVHHIBKUMWTI-OTMQOFQLSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain P [auth B]	G [auth A], P [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain G [auth A] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain P [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain L [auth B]	C [auth A], L [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain R [auth B] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] mmCIF format, chain J [auth A] mmCIF format, chain R [auth B]	J [auth A], R [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain R [auth B] Interactions & Density Focus chain J [auth A] Focus chain R [auth B]