Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.71 kDa 
• Atom Count: 1083 
• Residue Count: 124 
• Unique protein chains: 1

1A15

SDF-1ALPHA

• DOI: 10.2210/pdb1A15/pdb

• Classification: CHEMOKINE
• Mutation(s): Yes 


• Deposited: 1997-12-22 Released: 1998-08-12 
• Deposition Author(s): Dealwis, C.G., Fernandez, E.J., Lolis, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.298 
• R-Value Work: 0.233 
• R-Value Observed: 0.233 

Literature

Crystal structure of chemically synthesized [N33A] stromal cell-derived factor 1alpha, a potent ligand for the HIV-1 "fusin" coreceptor.

Dealwis, C., Fernandez, E.J., Thompson, D.A., Simon, R.J., Siani, M.A., Lolis, E.

(1998) Proc Natl Acad Sci U S A 95: 6941-6946

• PubMed: 9618518 
• DOI: 10.1073/pnas.95.12.6941
• Primary Citation of Related Structures:  
  1A15


• PubMed Abstract: 
  

Stromal cell-derived factor-1alpha (SDF-1alpha ) is a member of the chemokine superfamily and functions as a growth factor and chemoattractant through activation of CXCR4/LESTR/Fusin, a G protein-coupled receptor. This receptor also functions as a coreceptor for T-tropic syncytium-inducing strains of HIV-1. SDF-1alpha antagonizes infectivity of these strains by competing with gp120 for binding to the receptor. The crystal structure of a variant SDF-1alpha ([N33A]SDF-1alpha ) prepared by total chemical synthesis has been refined to 2.2-A resolution. Although SDF-1alpha adopts a typical chemokine beta-beta-beta-alpha topology, the packing of the alpha-helix against the beta-sheet is strikingly different. Comparison of SDF-1alpha with other chemokine structures confirms the hypothesis that SDF-1alpha may be either an ancestral protein from which all other chemokines evolved or the chemokine that is the least divergent from a primordial chemokine. The structure of SDF-1alpha reveals a positively charged surface ideal for binding to the negatively charged extracellular loops of the CXCR4 HIV-1 coreceptor. This ionic complementarity is likely to promote the interaction of the mobile N-terminal segment of SDF-1alpha with interhelical sites of the receptor, resulting in a biological response.

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Organizational Affiliation: 

Department of Pharmacology, Yale University School of Medicine, New Haven CT 06510, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STROMAL DERIVED FACTOR-1ALPHA	A, B	67	N/A	Mutation(s): 1
Find proteins for P48061 (Homo sapiens) Explore P48061  Go to UniProtKB:  P48061
NIH Common Fund Data Resources
PHAROS:  P48061 GTEx:  ENSG00000107562

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.298 
• R-Value Work: 0.233 
• R-Value Observed: 0.233 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.84	α = 90
b = 50.47	β = 90
c = 64.72	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-12-22 
• Released Date: 1998-08-12 
Deposition Author(s): Dealwis, C.G., Fernandez, E.J., Lolis, E.

Revision History 

• Version 1.0: 1998-08-12
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance