8HNK image
Deposition Date 2022-12-08
Release Date 2023-11-29
Last Version Date 2024-10-16
Entry Detail
PDB ID:
8HNK
Keywords:
SIGNALING PROTEIN
Title:
CXCR3-DNGi complex activated by CXCL11
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Escherichia coli (Taxon ID: 562)
Oplophorus gracilirostris (Taxon ID: 727944)
Host Organism:
Spodoptera frugiperda
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.01 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8HNK validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein G(i) subunit alpha-1
Gene (Uniprot):GNAI1
Chain IDs:A
Chain Length:354
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P63096 Pfam ID:PF00503
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:B
Chain Length:384
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62873 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Gene (Uniprot):GNG2
Chain IDs:C (auth: G)
Chain Length:71
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P59768 Pfam ID:PF00631
Protein Blast
Polymer Type:polypeptide(L)
Molecule:C-X-C motif chemokine 11
Gene (Uniprot):CXCL11
Chain IDs:E (auth: L)
Chain Length:104
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O14625 Pfam ID:PF00048
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Soluble cytochrome b562,C-X-C chemokine receptor type 3,Oplophorus-luciferin 2-monooxygenase catalytic subunit
Gene (Uniprot):cybC, CXCR3
Chain IDs:D (auth: R)
Chain Length:657
Number of Molecules:1
Biological Source:Escherichia coli, Homo sapiens, Oplophorus gracilirostris
UniProt ID:P0ABE7,P49682,Q9GV45 Pfam ID:PF07361, PF00001 EC:1.13.12.13
Polymer Type:polypeptide(L)
Molecule:single-chain variable fragment scFv16
Chain IDs:F (auth: S)
Chain Length:259
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
CLR
Primary Citation
Structural insights into the activation and inhibition of CXC chemokine receptor 3.
Nat.Struct.Mol.Biol. 31 610 620 (2024)
PMID: 38177682 DOI: 10.1038/s41594-023-01175-5

Abstact

The chemotaxis of CD4+ type 1 helper cells and CD8+ cytotoxic lymphocytes, guided by interferon-inducible CXC chemokine 9-11 (CXCL9-11) and CXC chemokine receptor 3 (CXCR3), plays a critical role in type 1 immunity. Here we determined the structures of human CXCR3-DNGi complexes activated by chemokine CXCL11, peptidomimetic agonist PS372424 and biaryl-type agonist VUF11222, and the structure of inactive CXCR3 bound to noncompetitive antagonist SCH546738. Structural analysis revealed that PS372424 shares a similar orthosteric binding pocket to the N terminus of CXCL11, while VUF11222 buries deeper and activates the receptor in a distinct manner. We showed an allosteric binding site between TM5 and TM6, accommodating SCH546738 in the inactive CXCR3. SCH546738 may restrain the receptor at an inactive state by preventing the repacking of TM5 and TM6. By revealing the binding patterns and the pharmacological properties of the four modulators, we present the activation mechanisms of CXCR3 and provide insights for future drug development.

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Primary Citation of related structures
8HNK