4RWS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.249 

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

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-X-C chemokine receptor type 4/Endolysin chimeric protein
A
498Homo sapiensEnterobacteria phage T4
This entity is chimeric
Gene Names: CXCR4, E
EC: 3.2.1.17
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
CXCR4 chemokine receptor complexed with IT1t antagonist
Find proteins for P61073 (Homo sapiens)
Go to Gene View: CXCR4
Go to UniProtKB:  P61073
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Viral macrophage inflammatory protein 2
C
80Human herpesvirus 8 type P (isolate GK18)Gene Names: ORF K4
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
CXCR4 chemokine receptor complexed with IT1t antagonist
Find proteins for Q98157 (Human herpesvirus 8 type P (isolate GK18))
Go to UniProtKB:  Q98157
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.249 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 82.320α = 90.00
b = 121.827β = 90.00
c = 189.766γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
BUSTERrefinement
HKL-2000data reduction
PHASERphasing
Blu-Icedata collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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