Macromolecule Content

• Total Structure Weight: 8.34 kDa 
• Atom Count: 504 
• Residue Count: 61 
• Unique protein chains: 1

1VMC

STROMA CELL-DERIVED FACTOR-1ALPHA (SDF-1ALPHA)

• DOI: 10.2210/pdb1VMC/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-09-20 Released: 2005-03-01 
• Deposition Author(s): Gozansky, E.K., Clore, G.M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 1 
• Selection Criteria: RESTRAINED REGULARIZED MEAN STRUCTURE 

Literature

Mapping the binding of the N-terminal extracellular tail of the CXCR4 receptor to stromal cell-derived factor-1alpha.

Gozansky, E.K., Louis, J.M., Caffrey, M., Clore, G.M.

(2005) J Mol Biol 345: 651-658

• PubMed: 15588815 
• DOI: 10.1016/j.jmb.2004.11.003
• Primary Citation of Related Structures:  
  1VMC


• PubMed Abstract: 
  

The solution structure of monomeric stromal cell-derived factor-1alpha (SDF-1alpha), the natural ligand for the CXCR4 G-coupled receptor, has been solved by multidimensional heteronuclear NMR spectroscopy. The structure has a characteristic chemokine fold and is in excellent agreement with the individual subunits observed in the crystal structures of dimeric SDF-1alpha. Using various peptides derived from the N-terminal extracellular tail of the CXCR4 receptor, we show that the principal determinants of binding reside in the N-terminal 17 residues of CXCR4, with a major contribution from the first six residues. From 15N/1HN chemical shift pertubation studies we show that the interaction surface on SDF-1alpha is formed by the undersurface of the three-stranded antiparallel beta-sheet bounded by the N-terminal loop on one side and the C-terminal helix on the other. This surface overlaps with but is not identical to that mapped on several other chemokines for the binding of equivalent peptides derived from their respective receptors.

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Organizational Affiliation: 

Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD 20892-0520, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stromal cell-derived factor 1	A	71	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: 100 
• Conformers Submitted: 1 
• Selection Criteria: RESTRAINED REGULARIZED MEAN STRUCTURE 
• OLDERADO: 1VMC Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-09-20 
• Released Date: 2005-03-01 
Deposition Author(s): Gozansky, E.K., Clore, G.M.

Revision History 

• Version 1.0: 2005-03-01
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance