8K3Z | pdb_00008k3z

Cryo-EM structure of CXCR4 in complex with CXCL12


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryo-EM structure of monomeric CXCL12-bound CXCR4 in the active state.

Liu, Y.Liu, A.Li, X.Liao, Q.Zhang, W.Zhu, L.Ye, R.D.

(2024) Cell Rep 43: 114578-114578

  • DOI: https://doi.org/10.1016/j.celrep.2024.114578
  • Primary Citation of Related Structures:  
    8K3Z

  • PubMed Abstract: 

    CXCR4 binding of its endogenous agonist CXCL12 leads to diverse functions, including bone marrow retention of hematopoietic progenitors and cancer metastasis. However, the structure of the CXCL12-bound CXCR4 remains unresolved despite available structures of CXCR4 in complex with antagonists. Here, we present the cryoelectron microscopy (cryo-EM) structure of the CXCL12-CXCR4-Gi complex at an overall resolution of 2.65 Å. CXCL12 forms a 1:1 stoichiometry complex with CXCR4, following the two-site model. The first 8 amino acids of mature CXCL12 are crucial for CXCR4 activation by forming polar interactions with minor sub-pocket residues in the transmembrane binding pocket. The 3.2-Å distance between V3 of CXCL12 and the "toggle switch" W 6.48 marks the deepest insertion among all chemokine-receptor pairs, leading to conformational changes of CXCR4 for G protein activation. These results, combined with functional assays and computational analysis, provide the structural basis for CXCR4 activation by CXCL12.


  • Organizational Affiliation
    • Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-X-C chemokine receptor type 4296Homo sapiensMutation(s): 0 
Gene Names: CXCR4
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P61073 (Homo sapiens)
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Go to UniProtKB:  P61073
PHAROS:  P61073
GTEx:  ENSG00000121966 
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UniProt GroupP61073
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1338Homo 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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Stromal cell-derived factor 162Homo sapiensMutation(s): 0 
Gene Names: CXCL12SDF1SDF1ASDF1B
Membrane Entity: Yes 
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Find proteins for P48061 (Homo sapiens)
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PHAROS:  P48061
GTEx:  ENSG00000107562 
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UniProt GroupP48061
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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]55Homo 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 S]247Vicugna pacosMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-01-29
    Changes: Data collection, Database references
  • Version 1.3: 2025-07-02
    Changes: Data collection