9KHH | pdb_00009khh

Structure of the complex of LGR4 with Norrin (2:2)

PDB DOI: https://doi.org/10.2210/pdb9KHH/pdb
EM Map EMD-62340: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Camelus dromedarius, Homo sapiens
Expression System: Escherichia coli, Spodoptera frugiperda, Homo sapiens
Mutation(s): No

Deposited: 2024-11-10 Released: 2025-07-16
Deposition Author(s): Yong, G., Hu, F.Z., Qiao, H.R.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.65 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9KHH

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

Literature

Structure of the complex of LGR4 with Norrin (2:2)

Yong, G., Hu, F.Z., Qiao, H.R.

To be published.

Macromolecule Content

Total Structure Weight: 419.95 kDa
Atom Count: 12,354
Modeled Residue Count: 1,871
Deposited Residue Count: 3,838
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MB52	A, D [auth B]	556	Camelus dromedarius	Mutation(s): 0

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Norrin,Immunoglobulin gamma-1 heavy chain	B [auth E], C [auth F]	409	Homo sapiens	Mutation(s): 0 Gene Names: NDP, EVR2
UniProt & NIH Common Fund Data Resources
Find proteins for Q00604 (Homo sapiens) Explore Q00604 Go to UniProtKB: Q00604
PHAROS: Q00604 GTEx: ENSG00000124479
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00604
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat-containing G-protein coupled receptor 4	E [auth C], F [auth D]	954	Homo sapiens	Mutation(s): 0 Gene Names: LGR4, GPR48
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXB1 (Homo sapiens) Explore Q9BXB1 Go to UniProtKB: Q9BXB1
PHAROS: Q9BXB1 GTEx: ENSG00000205213
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BXB1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.65 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-07-16
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.