Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65.75 kDa 
• Atom Count: 3953 
• Modelled Residue Count: 508 
• Deposited Residue Count: 578 
• Unique protein chains: 2

4RWS

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

• PDB DOI: 10.2210/pdb4RWS/pdb

• Classification: SIGNALING PROTEIN, HYDROLASE
• Organism(s): Homo sapiens, Escherichia virus T4, Human herpesvirus 8 strain GK18
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMMemProtMDmpstruc


• Deposited: 2014-12-05 Released: 2015-02-11 
• Deposition Author(s): Qin, L., Kufareva, I., Holden, L., Wang, C., Zheng, Y., Wu, H., Fenalti, G., Han, G.W., Cherezov, V., Abagyan, R., Stevens, R.C., Handel, T.M., GPCR Network (GPCR)

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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 

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

• PubMed: 25612609 
• 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. 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.

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Organizational Affiliation: 

University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA. [e-mail] [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-X-C chemokine receptor type 4/Endolysin chimeric protein	A	498	Homo sapiens, Escherichia virus T4	Mutation(s): 5  Gene Names: CXCR4, E 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
UniProt Groups	P61073P00720

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Viral macrophage inflammatory protein 2	B [auth C]	80	Human herpesvirus 8 strain GK18	Mutation(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

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 = 82.32	α = 90
b = 121.827	β = 90
c = 189.766	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-12-05 
• Released Date: 2015-02-11 
Deposition Author(s): Qin, L., Kufareva, I., Holden, L., Wang, C., Zheng, Y., Wu, H., Fenalti, G., Han, G.W., Cherezov, V., Abagyan, R., Stevens, R.C., Handel, T.M., GPCR Network (GPCR)

Revision History  

• 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