9AST | pdb_00009ast

Cryo-EM structure of XCR1 signaling complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 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

Molecular basis for chemokine recognition and activation of XCR1.

Zhang, X.Schlimgen, R.R.Singh, S.Tomani, M.P.Volkman, B.F.Zhang, C.

(2024) Proc Natl Acad Sci U S A 121: e2405732121-e2405732121

  • DOI: https://doi.org/10.1073/pnas.2405732121
  • Primary Citation of Related Structures:  
    9AST

  • PubMed Abstract: 

    The X-C motif chemokine receptor XCR1, which selectively binds to the chemokine XCL1, is highly expressed in conventional dendritic cells subtype 1 (cDC1s) and crucial for their activation. Modulating XCR1 signaling in cDC1s could offer novel opportunities in cancer immunotherapy and vaccine development by enhancing the antigen presentation function of cDC1s. To investigate the molecular mechanism of XCL-induced XCR1 signaling, we determined a high-resolution structure of the human XCR1 and G i complex with an engineered form of XCL1, XCL1 CC3, by cryoelectron microscopy. Through mutagenesis and structural analysis, we elucidated the molecular details for the binding of the N-terminal segment of XCL1 CC3, which is vital for activating XCR1. The unique arrangement within the XCL1 CC3 binding site confers specificity for XCL1 in XCR1. We propose an activation mechanism for XCR1 involving structural alterations of key residues at the bottom of the XCL1 binding pocket. These detailed insights into XCL1 CC3-XCR1 interaction and XCR1 activation pave the way for developing novel XCR1-targeted therapeutics.


  • Organizational Affiliation
    • Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(s): 4 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
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Find proteins for P63096 (Homo sapiens)
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PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LymphotactinB [auth L]133Homo sapiensMutation(s): 0 
Gene Names: XCL1LTNSCYC1
Membrane Entity: Yes 
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Find proteins for P47992 (Homo sapiens)
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PHAROS:  P47992
GTEx:  ENSG00000143184 
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UniProt GroupP47992
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chemokine XC receptor 1,Non structural polyproteinC [auth R]532Homo sapiensMutation(s): 0 
Gene Names: XCR1CCXCR1GPR5
Membrane Entity: Yes 
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Find proteins for P46094 (Homo sapiens)
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PHAROS:  P46094
GTEx:  ENSG00000173578 
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UniProt GroupsA0A482LYE4P46094
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1D [auth B]351Homo sapiensMutation(s): 0 
Gene Names: GNB1
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PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2E [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16F [auth E]266Mus musculusMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM128641

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release