1SDF

SOLUTION STRUCTURE OF STROMAL CELL-DERIVED FACTOR-1 (SDF-1), NMR, MINIMIZED AVERAGE STRUCTURE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 
  • Selection Criteria: AVERAGE STRUCTURE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure and basis for functional activity of stromal cell-derived factor-1; dissociation of CXCR4 activation from binding and inhibition of HIV-1.

Crump, M.P.Gong, J.H.Loetscher, P.Rajarathnam, K.Amara, A.Arenzana-Seisdedos, F.Virelizier, J.L.Baggiolini, M.Sykes, B.D.Clark-Lewis, I.

(1997) EMBO J. 16: 6996-7007

  • DOI: 10.1093/emboj/16.23.6996
  • Primary Citation of Related Structures:  2SDF

  • PubMed Abstract: 
  • The three-dimensional structure of stromal cell-derived factor-1 (SDF-1) was determined by NMR spectroscopy. SDF-1 is a monomer with a disordered N-terminal region (residues 1-8), and differs from other chemokines in the packing of the hydrophobic co ...

    The three-dimensional structure of stromal cell-derived factor-1 (SDF-1) was determined by NMR spectroscopy. SDF-1 is a monomer with a disordered N-terminal region (residues 1-8), and differs from other chemokines in the packing of the hydrophobic core and surface charge distribution. Results with analogs showed that the N-terminal eight residues formed an important receptor binding site; however, only Lys-1 and Pro-2 were directly involved in receptor activation. Modification to Lys-1 and/or Pro-2 resulted in loss of activity, but generated potent SDF-1 antagonists. Residues 12-17 of the loop region, which we term the RFFESH motif, unlike the N-terminal region, were well defined in the SDF-1 structure. The RFFESH formed a receptor binding site, which we propose to be an important initial docking site of SDF-1 with its receptor. The ability of the SDF-1 analogs to block HIV-1 entry via CXCR4, which is a HIV-1 coreceptor for the virus in addition to being the receptor for SDF-1, correlated with their affinity for CXCR4. Activation of the receptor is not required for HIV-1 inhibition.


    Organizational Affiliation

    Protein Engineering Network of Centers of Excellence (PENCE) and Department of Biochemistry, 713 Heritage Medical Research Center, University of Alberta, Edmonton, Alberta, Canada T6G 2S2.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
STROMAL CELL-DERIVED FACTOR-1
A
67Homo sapiensGene Names: CXCL12 (SDF1, SDF1A, SDF1B)
Find proteins for P48061 (Homo sapiens)
Go to Gene View: CXCL12
Go to UniProtKB:  P48061
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 
  • Selection Criteria: AVERAGE STRUCTURE 
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance