8XGM image
Deposition Date 2023-12-15
Release Date 2024-08-21
Last Version Date 2025-07-02
Entry Detail
PDB ID:
8XGM
Title:
Cryo-EM structure of human GPR1 bound to chemerin
Biological Source:
Source Organism:
Vicugna pacos (Taxon ID: 30538)
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.29 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:G-protein coupled receptor 1
Gene (Uniprot):CMKLR2
Chain IDs:B (auth: A)
Chain Length:306
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Gene (Uniprot):GNB1
Chain IDs:C (auth: B)
Chain Length:340
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein G(i) subunit alpha-1
Gene (Uniprot):GNAI1
Mutagens:G203A, A326S
Chain IDs:D (auth: C)
Chain Length:354
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Retinoic acid receptor responder protein 2
Gene (Uniprot):RARRES2
Chain IDs:F (auth: D)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein subunit gamma
Chain IDs:E (auth: G)
Chain Length:55
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:scFV16
Chain IDs:A (auth: S)
Chain Length:247
Number of Molecules:1
Biological Source:Vicugna pacos
Ligand Molecules
Primary Citation
Structure of G protein-coupled receptor GPR1 bound to full-length chemerin adipokine reveals a chemokine-like reverse binding mode.
Plos Biol. 22 e3002838 e3002838 (2024)
PMID: 39466725 DOI: 10.1371/journal.pbio.3002838

Abstact

Chemerin is an adipokine with chemotactic activity to a subset of leukocytes. Chemerin binds to 3 G protein-coupled receptors, including chemokine-like receptor 1 (CMKLR1), G protein-coupled receptor 1 (GPR1), and C-C chemokine receptor-like 2 (CCRL2). Here, we report that GPR1 is capable of Gi signaling when stimulated with full-length chemerin or its C-terminal nonapeptide (C9, YFPGQFAFS). We present high-resolution cryo-EM structures of Gi-coupled GPR1 bound to full-length chemerin and to the C9 peptide, respectively. C9 insertion into the transmembrane (TM) binding pocket is both necessary and sufficient for GPR1 signaling, whereas the full-length chemerin uses its bulky N-terminal core for interaction with a β-strand located at the N-terminus of GPR1. This interaction involves multiple β-strands of full-length chemerin, forming a β-sheet that serves as a "lid" for the TM binding pocket and is energetically expensive to remove as indicated by molecular dynamics simulations with free energy landscape analysis. Combining results from functional assays, our structural model explains why C9 is an activating peptide at GPR1 and how the full-length chemerin uses a "two-site" model for enhanced interaction with GPR1.

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Primary Citation of related structures