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)

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Experimental Data Snapshot

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

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 16: 381-385

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

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Organizational Affiliation: 
• School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
Lingang Laboratory, Shanghai 200000, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

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

Macromolecules

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 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 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

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

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

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Zhu, Y., He, M., Wu, B., Zhao, Q.

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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

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release
  
• Version 1.1: 2025-06-11
  Changes: Data collection, Database references