3OE0

Crystal structure of the CXCR4 chemokine receptor in complex with a cyclic peptide antagonist CVX15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


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

  • DOI: 10.1126/science.1194396
  • Structures With Same Primary Citation

  • 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. He ...

    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.


    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
MoleculeChainsSequence LengthOrganismDetails
C-X-C chemokine receptor type 4, Lysozyme ChimeraA499Homo sapiensEscherichia virus T4Mutation(s): 4 
Gene Names: CXCR4CXCR4_HUMANE
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)
Explore P61073 
Go to UniProtKB:  P61073
NIH Common Fund Data Resources
PHAROS  P61073
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyphemusin analog, CXC chemokine receptor antagonistI16N/AMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001107
Query on PRD_001107
IPolyphemusin analog, CXC chemokine receptor antagonistO /  Antagonist

--

Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ALN
Query on ALN
IL-PEPTIDE LINKINGC13 H13 N O2ALA
CIR
Query on CIR
IL-PEPTIDE LINKINGC6 H13 N3 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.08α = 90
b = 144.86β = 104.54
c = 73.99γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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: 2012-12-12
    Changes: Other
  • Version 1.4: 2017-07-26
    Changes: Refinement description, Source and taxonomy