9L3Z | pdb_00009l3z

Cryo-EM structure of the inactive chemokine-like receptor 1 (CMKLR1)

PDB DOI: https://doi.org/10.2210/pdb9L3Z/pdb
EM Map EMD-62799: EMDB EMDataResource

Classification: MEMBRANE PROTEIN/IMMUNE SYSTEM
Organism(s): Mus musculus, Homo sapiens, Escherichia coli
Expression System: Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes PDBTM

Deposited: 2024-12-19 Released: 2025-03-12
Deposition Author(s): Zhu, Y., He, M., Wu, B., Zhao, Q.
Funding Organization(s): National Science Foundation (NSF, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 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 the distinct ligand recognition and signaling of the chemerin receptors CMKLR1 and GPR1.

Lin, X., Zhao, L., Cai, H., Chang, X., Tang, Y., Luo, T., Wu, M., Yi, C., Ma, L., Chu, X., Han, S., Zhao, Q., Wu, B., He, M., Zhu, Y.

(2025) Protein Cell

PubMed: 39752296 Search on PubMed
DOI: https://doi.org/10.1093/procel/pwae073
Primary Citation of Related Structures:
9L3W, 9L3Y, 9L3Z

Organizational Affiliation

School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.

Macromolecule Content

Total Structure Weight: 107.45 kDa
Atom Count: 5,147
Modelled Residue Count: 734
Deposited Residue Count: 973
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
The heavy chain of anti-BRIL Fab	A [auth H]	252	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
The light chain of anti-BRIL Fab	B [auth L]	216	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Chemerin-like receptor 1,Soluble cytochrome b562	C [auth A]	498	Homo sapiens, Escherichia coli	Mutation(s): 1 Gene Names: CMKLR1, CHEMR23, DEZ, cybC Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q99788 (Homo sapiens) Explore Q99788 Go to UniProtKB: Q99788
PHAROS: Q99788 GTEx: ENSG00000174600
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P0ABE7Q99788
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
LRH7-C2	D [auth C]	7	Homo sapiens	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-12

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	2022YFA1302900
National Natural Science Foundation of China (NSFC)	China	82121005
National Natural Science Foundation of China (NSFC)	China	32401012