Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65746.21 
• Atom Count: 3953 
• Residue Count: 578 
• Unique protein chains: 2

4RWS

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

• DOI: 10.2210/pdb4RWS/pdb

• Classification: SIGNALING PROTEIN HYDROLASE
• Organism(s): Human herpesvirus 8 type P, Homo sapiens, Enterobacteria phage T4
• Expression System: Spodoptera frugiperda
• Mutation(s): 6 


• 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: 3.1 Å
• R-Value Free: 0.274 
• R-Value Work: 0.249 

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


• 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
C-X-C chemokine receptor type 4/Endolysin chimeric protein	A	498	Homo sapiens, Enterobacteria phage T4 This entity is chimeric	Mutation(s): 5  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
Molecule	Chains	Sequence Length	Organism	Details
Viral macrophage inflammatory protein 2	C	80	Human herpesvirus 8 type P	Mutation(s): 1  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) 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 = 82.320	α = 90.00
b = 121.827	β = 90.00
c = 189.766	γ = 90.00

Software Package:

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