8Z8Z | pdb_00008z8z

Cryo-EM structure of LYCHOS


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

  • DOI: https://doi.org/10.1038/s41594-024-01474-5
  • Primary Citation of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysosomal cholesterol signaling protein,Fluorescent Protein
A, B
1,144Homo sapienssynthetic construct
This entity is chimeric
Mutation(s): 0 
Gene Names: GPR155PGR22
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z3F1
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q7Z3F1-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L1C (Subject of Investigation/LOI)
Query on A1L1C

Download Ideal Coordinates CCD File 
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
LBN
Query on LBN

Download Ideal Coordinates CCD File 
I [auth A],
K [auth B]
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
C42 H82 N O8 P
WTJKGGKOPKCXLL-VYOBOKEXSA-N
6OU
Query on 6OU

Download Ideal Coordinates CCD File 
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
CLR
Query on CLR

Download Ideal Coordinates CCD File 
G [auth A],
P [auth B]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
L [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth A],
R [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82151215

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release
  • Version 1.1: 2025-02-05
    Changes: Data collection, Database references
  • Version 1.2: 2025-06-04
    Changes: Data collection, Database references
  • Version 1.3: 2025-06-25
    Changes: Data collection