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

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This is version 1.3 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: https://doi.org/10.1093/emboj/16.23.6996
  • Primary Citation of Related Structures:  
    1SDF, 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
STROMAL CELL-DERIVED FACTOR-167Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P48061 (Homo sapiens)
Explore P48061 
Go to UniProtKB:  P48061
PHAROS:  P48061
GTEx:  ENSG00000107562 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48061
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Database references, Derived calculations, Other