9JBH | pdb_00009jbh

Cryo-EM structure of the human LYCHOS PLD homodimer

PDB DOI: https://doi.org/10.2210/pdb9JBH/pdb
EM Map EMD-61314: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-08-27 Released: 2025-07-16
Deposition Author(s): Yu, S., Liang, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.73 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 insights into cholesterol sensing by the LYCHOS-mTORC1 pathway

Yu, S., Liang, L.

To be published.

Macromolecule Content

Total Structure Weight: 91.15 kDa
Atom Count: 5,724
Modeled Residue Count: 668
Deposited Residue Count: 756
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysosomal cholesterol signaling protein	A, B	378	Homo sapiens	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7Z3F1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL (Subject of Investigation/LOI) Query on CDL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
3PE (Subject of Investigation/LOI) Query on 3PE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	C [auth A] E [auth A] F [auth A] G [auth B] I [auth B] C [auth A], E [auth A], F [auth A], G [auth B], I [auth B], J [auth B]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth B] Focus chain J [auth B]