4RWS

Crystal structure of CXCR4 and viral chemokine antagonist vMIP-II complex (PSI Community Target)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural biology. Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine.

Qin, L.Kufareva, I.Holden, L.G.Wang, C.Zheng, Y.Zhao, C.Fenalti, G.Wu, H.Han, G.W.Cherezov, V.Abagyan, R.Stevens, R.C.Handel, T.M.

(2015) Science 347: 1117-1122

  • DOI: 10.1126/science.1261064
  • Primary Citation of Related Structures:  
    4RWS

  • PubMed Abstract: 
  • Chemokines and their receptors control cell migration during development, immune system responses, and in numerous diseases, including inflammation and cancer. The structural basis of receptor:chemokine recognition has been a long-standing unanswered question due to the challenges of structure determination for membrane protein complexes ...

    Chemokines and their receptors control cell migration during development, immune system responses, and in numerous diseases, including inflammation and cancer. The structural basis of receptor:chemokine recognition has been a long-standing unanswered question due to the challenges of structure determination for membrane protein complexes. Here, we report the crystal structure of the chemokine receptor CXCR4 in complex with the viral chemokine antagonist vMIP-II at 3.1 angstrom resolution. The structure revealed a 1:1 stoichiometry and a more extensive binding interface than anticipated from the paradigmatic two-site model. The structure helped rationalize a large body of mutagenesis data and together with modeling provided insights into CXCR4 interactions with its endogenous ligand CXCL12, its ability to recognize diverse ligands, and the specificity of CC and CXC receptors for their respective chemokines.


    Organizational Affiliation

    University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA. thandel@ucsd.edu stevens@usc.edu ikufareva@ucsd.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C-X-C chemokine receptor type 4/Endolysin chimeric proteinA498Homo sapiensEscherichia virus T4Mutation(s): 5 
Gene Names: CXCR4E
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P61073 (Homo sapiens)
Explore P61073 
Go to UniProtKB:  P61073
PHAROS:  P61073
GTEx:  ENSG00000121966 
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP61073P00720
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Viral macrophage inflammatory protein 2B [auth C]80Human herpesvirus 8 strain GK18Mutation(s): 1 
Gene Names: ORF K4
Membrane Entity: Yes 
UniProt
Find proteins for Q98157 (Human herpesvirus 8 type P (isolate GK18))
Explore Q98157 
Go to UniProtKB:  Q98157
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ98157
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.32α = 90
b = 121.827β = 90
c = 189.766γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Database references
  • Version 1.2: 2015-04-15
    Changes: Database references
  • Version 1.3: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2017-11-22
    Changes: Refinement description