Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 118216.37 
• Atom Count: 7662 
• Residue Count: 1004 
• Unique protein chains: 1

3ODU

The 2.5 A structure of the CXCR4 chemokine receptor in complex with small molecule antagonist IT1t

• DOI: 10.2210/pdb3ODU/pdb

• Classification: SIGNALING PROTEIN HYDROLASE
• Organism(s): Homo sapiens, Enterobacteria phage T4
• Expression System: Spodoptera frugiperda
• Mutation(s): 3 


• Deposited: 2010-08-11 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: 2.5 Å
• R-Value Free: 0.282 
• R-Value Work: 0.237 

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:  
  3OE8, 3OE9, 3OE6, 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
C-X-C chemokine receptor type 4, Lysozyme Chimera	A, B	502	Homo sapiens, Enterobacteria phage T4 This entity is chimeric	Mutation(s): 3  Gene Names: CXCR4, E EC: 3.2.1.17
Membrane protein mpstruc	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
OLC	A, B	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate 1-Oleoyl-R-glycerol C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA	A, B	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
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: 1.1 - 11 nM (93) BINDINGDB
ITD	Ki: 7.3 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.282 
• R-Value Work: 0.237 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 64.540	α = 90.00
b = 83.692	β = 102.17
c = 119.995	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-08-11 
• 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
  Type: Version format compliance
• Version 1.2: 2012-05-02
  Type: Structure summary
• Version 1.3: 2017-07-26
  Type: Refinement description, Source and taxonomy