Macromolecule Content

• Total Structure Weight: 7.85 kDa 
• Atom Count: 550 
• Modelled Residue Count: 67 
• Deposited Residue Count: 67 
• Unique protein chains: 1

1SDF

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

• DOI: 10.2210/pdb1SDF/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1997-11-15 Released: 1998-01-28 
• Deposition Author(s): Crump, M.P., Rajarathnam, K., Clark-Lewis, I., Sykes, B.D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 30 
• Conformers Submitted: 1 
• Selection Criteria: AVERAGE STRUCTURE 

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

• PubMed: 9384579 
• DOI: 10.1093/emboj/16.23.6996
• Primary Citation of Related Structures:  
  2SDF, 1SDF


• 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STROMAL CELL-DERIVED FACTOR-1	A	67	Homo sapiens	Mutation(s): 0  Gene Names: CXCL12, SDF1, SDF1A, SDF1B
Find proteins for P48061 (Homo sapiens) Explore P48061  Go to UniProtKB:  P48061
NIH Common Fund Data Resources
PHAROS:  P48061 GTEx:  ENSG00000107562

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 30 
• Conformers Submitted: 1 
• Selection Criteria: AVERAGE STRUCTURE 
• OLDERADO: 1SDF Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-11-15 
• Released Date: 1998-01-28 
Deposition Author(s): Crump, M.P., Rajarathnam, K., Clark-Lewis, I., Sykes, B.D.

Revision History  

• 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