Biological Assembly 1  

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: 118.22 kDa 
• Atom Count: 7,805 
• Modelled Residue Count: 922 
• Deposited Residue Count: 1,004 
• Unique protein chains: 1

 3ODU

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

• PDB DOI: 10.2210/pdb3ODU/pdb

• Classification: SIGNALING PROTEIN, HYDROLASE
• Organism(s): Homo sapiens, Tequatrovirus T4
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• 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: 2.50 Å
• R-Value Free: 0.282 
• R-Value Work: 0.237 
• R-Value Observed: 0.240 

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:  
  3ODU, 3OE0, 3OE6, 3OE8, 3OE9


• 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	502	Homo sapiens, Tequatrovirus T4	Mutation(s): 3  Gene Names: CXCR4, CXCR4_HUMAN, 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
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720
UniProt Groups	P61073P00720

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ITD	C [auth A], H [auth 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
OLC	D [auth A], E [auth A], F [auth A], I [auth B], J [auth B]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA	G [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ITD	PDBBind:  3ODU	Ki: 7.3 (nM) from 1 assay(s)
	BindingDB:  3ODU	IC50: min: 1.1, max: 7400 (nM) from 14 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.282 
• R-Value Work: 0.237 
• R-Value Observed: 0.240 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.54	α = 90
b = 83.692	β = 102.17
c = 119.995	γ = 90

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

• 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
• Version 1.4: 2021-10-06
  Changes: Database references, Derived calculations