9L3Y | pdb_00009l3y

Cryo-EM structure of the G-protein coupled receptor 1 (GPR1) in complex with chemerin and Gi1

PDB DOI: https://doi.org/10.2210/pdb9L3Y/pdb
EM Map EMD-62798: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
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: 3.60 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: 144.4 kDa
Atom Count: 7,383
Modelled Residue Count: 993
Deposited Residue Count: 1,270
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chemerin-like receptor 2	A [auth R]	368	Homo sapiens	Mutation(s): 0 Gene Names: CMKLR2, GPR1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P46091 (Homo sapiens) Explore P46091 Go to UniProtKB: P46091
PHAROS: P46091 GTEx: ENSG00000183671
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P46091
Sequence Annotations Expand
Reference Sequence LOADING

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid receptor responder protein 2	B [auth L]	137	Homo sapiens	Mutation(s): 0 Gene Names: RARRES2, TIG2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q99969 (Homo sapiens) Explore Q99969 Go to UniProtKB: Q99969
PHAROS: Q99969 GTEx: ENSG00000106538
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99969
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	C [auth A]	354	Homo sapiens	Mutation(s): 5 Gene Names: GNAI1 EC: 3.6.5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096 Go to UniProtKB: P63096
PHAROS: P63096 GTEx: ENSG00000127955
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63096
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	D [auth B]	340	Homo sapiens	Mutation(s): 0 Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens) Explore P62873 Go to UniProtKB: P62873
PHAROS: P62873 GTEx: ENSG00000078369
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62873
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	E [auth C]	71	Homo sapiens	Mutation(s): 0 Gene Names: GNG2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768 Go to UniProtKB: P59768
PHAROS: P59768 GTEx: ENSG00000186469
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P59768
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158

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