Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 114.18 kDa 
• Atom Count: 6780 
• Residue Count: 835 
• Unique protein chains: 1

3OE9

Crystal structure of the chemokine CXCR4 receptor in complex with a small molecule antagonist IT1t in P1 spacegroup

• DOI: 10.2210/pdb3OE9/pdb

• Classification: SIGNALING PROTEIN, HYDROLASE
• Organism(s): Homo sapiens, Escherichia virus T4
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2010-08-12 Released: 2010-10-27 
• Deposition Author(s): Wu, B., Mol, C.D., Han, G.W., Katritch, V., Chien, E.Y.T., Liu, W., Cherezov, V., Stevens, R.C., Accelerated Technologies Center for Gene to 3D Structure (ATCG3D), GPCR Network (GPCR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.284 
• R-Value Work: 0.252 
• R-Value Observed: 0.254 

Literature

Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists.

Wu, B., Chien, E.Y., Mol, C.D., Fenalti, G., Liu, W., Katritch, V., Abagyan, R., Brooun, A., Wells, P., Bi, F.C., Hamel, D.J., Kuhn, P., Handel, T.M., Cherezov, V., Stevens, R.C.

(2010) Science 330: 1066-1071

• PubMed: 20929726 
• DOI: 10.1126/science.1194396
• Primary Citation of Related Structures:  
  3OE9, 3ODU, 3OE6, 3OE8, 3OE0


• PubMed Abstract: 
  

Chemokine receptors are critical regulators of cell migration in the context of immune surveillance, inflammation, and development. The G protein-coupled chemokine receptor CXCR4 is specifically implicated in cancer metastasis and HIV-1 infection. Here we report five independent crystal structures of CXCR4 bound to an antagonist small molecule IT1t and a cyclic peptide CVX15 at 2.5 to 3.2 angstrom resolution. All structures reveal a consistent homodimer with an interface including helices V and VI that may be involved in regulating signaling. The location and shape of the ligand-binding sites differ from other G protein-coupled receptors and are closer to the extracellular surface. These structures provide new clues about the interactions between CXCR4 and its natural ligand CXCL12, and with the HIV-1 glycoprotein gp120.

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Organizational Affiliation: 

Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-X-C chemokine receptor type 4, Lysozyme Chimera	A, B	499	Homo sapiens, Escherichia virus T4	Mutation(s): 4  Gene Names: CXCR4, CXCR4_HUMAN, E EC: 3.2.1.17
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors: Class A	Protein:  CXCR4 chemokine receptor complexed with IT1t antagonist
Find proteins for P61073 (Homo sapiens) Explore P61073  Go to UniProtKB:  P61073
NIH Common Fund Data Resources
PHAROS:  P61073 GTEx:  ENSG00000121966
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ITD	A, B	(6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl N,N'-dicyclohexylimidothiocarbamate C21 H34 N4 S2 OOSUDWRRWZVFEB-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ITD	IC50:  8   nM  BindingDB
ITD	IC50:  1.100000023841858   nM  BindingDB
ITD	Ki :  6.599999904632568   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.284 
• R-Value Work: 0.252 
• R-Value Observed: 0.254 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.497	α = 64.66
b = 72.739	β = 73.93
c = 84.273	γ = 61.31

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-08-12 
• Released Date: 2010-10-27 
Deposition Author(s): Wu, B., Mol, C.D., Han, G.W., Katritch, V., Chien, E.Y.T., Liu, W., Cherezov, V., Stevens, R.C., Accelerated Technologies Center for Gene to 3D Structure (ATCG3D), GPCR Network (GPCR)

Revision History 

• Version 1.0: 2010-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-05-02
  Changes: Structure summary
• Version 1.3: 2017-07-26
  Changes: Refinement description, Source and taxonomy