2NWG

Structure of CXCL12:heparin disaccharide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and Functional Basis of CXCL12 (Stromal Cell-derived Factor-1{alpha}) Binding to Heparin

Murphy, J.W.Cho, Y.Sachpatzidis, A.Fan, C.Hodsdon, M.E.Lolis, E.

(2007) J.Biol.Chem. 282: 10018-10027

  • DOI: 10.1074/jbc.M608796200

  • PubMed Abstract: 
  • CXCL12 (SDF-1alpha) and CXCR4 are critical for embryonic development and cellular migration in adults. These proteins are involved in HIV-1 infection, cancer metastasis, and WHIM disease. Sequestration and presentation of CXCL12 to CXCR4 by glycosami ...

    CXCL12 (SDF-1alpha) and CXCR4 are critical for embryonic development and cellular migration in adults. These proteins are involved in HIV-1 infection, cancer metastasis, and WHIM disease. Sequestration and presentation of CXCL12 to CXCR4 by glycosaminoglycans (GAGs) is proposed to be important for receptor activation. Mutagenesis has identified CXCL12 residues that bind to heparin. However, the molecular details of this interaction have not yet been determined. Here we demonstrate that soluble heparin and heparan sulfate negatively affect CXCL12-mediated in vitro chemotaxis. We also show that a cluster of basic residues in the dimer interface is required for chemotaxis and is a target for inhibition by heparin. We present structural evidence for binding of an unsaturated heparin disaccharide to CXCL12 attained through solution NMR spectroscopy and x-ray crystallography. Increasing concentrations of the disaccharide altered the two-dimensional (1)H-(15)N-HSQC spectra of CXCL12, which identified two clusters of residues. One cluster corresponds to beta-strands in the dimer interface. The second includes the amino-terminal loop and the alpha-helix. In the x-ray structure two unsaturated disaccharides are present. One is in the dimer interface with direct contacts between residues His(25), Lys(27), and Arg(41) of CXCL12 and the heparin disaccharide. The second disaccharide contacts Ala(20), Arg(21), Asn(30), and Lys(64). This is the first x-ray structure of a CXC class chemokine in complex with glycosaminoglycans. Based on the observation of two heparin binding sites, we propose a mechanism in which GAGs bind around CXCL12 dimers as they sequester and present CXCL12 to CXCR4.


    Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Stromal cell-derived factor 1
A, B
68Homo sapiensMutation(s): 0 
Gene Names: CXCL12 (SDF1, SDF1A, SDF1B)
Find proteins for P48061 (Homo sapiens)
Go to Gene View: CXCL12
Go to UniProtKB:  P48061
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H1S
Query on H1S

Download SDF File 
Download CCD File 
A
HEPARIN DISACCHARIDE I-S
C12 H15 N O19 S3
LRPGJWKAYQRIAQ-GYBHJADLSA-J
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.492α = 90.00
b = 56.965β = 90.00
c = 71.747γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CCP4data scaling
DENZOdata reduction
PHASERphasing
SCALEPACKdata scaling
CrystalCleardata collection
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description