Biological Assembly 1  

 3D View: Structure

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.42 kDa 
• Atom Count: 1723 
• Residue Count: 212 
• Unique protein chains: 2

2K04

Structure of SDF1 in complex with the CXCR4 N-terminus containing no sulfotyrosines

• DOI: 10.2210/pdb2K04/pdb
• BMRB: 15636

• Classification: CYTOKINE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-01-24 Released: 2008-10-28 
• Deposition Author(s): Volkman, B.F., Veldkamp, C.T., Peterson, F.C.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

Structural basis of CXCR4 sulfotyrosine recognition by the chemokine SDF-1/CXCL12

Veldkamp, C.T., Seibert, C., Peterson, F.C., De la Cruz, N.B., Haugner, J.C., Basnet, H., Sakmar, T.P., Volkman, B.F.

(2008) Sci Signal 1: ra4-ra4

• PubMed: 18799424 
• DOI: 10.1126/scisignal.1160755
• Primary Citation of Related Structures:  
  2K05, 2K04, 2K03, 2K01


• PubMed Abstract: 
  

Stem cell homing and breast cancer metastasis are orchestrated by the chemokine stromal cell-derived factor 1 (SDF-1) and its receptor CXCR4. Here, we report the nuclear magnetic resonance structure of a constitutively dimeric SDF-1 in complex with a CXCR4 fragment that contains three sulfotyrosine residues important for a high-affinity ligand-receptor interaction. CXCR4 bridged the SDF-1 dimer interface so that sulfotyrosines sTyr7 and sTyr12 of CXCR4 occupied positively charged clefts on opposing chemokine subunits. Dimeric SDF-1 induced intracellular Ca2+ mobilization but had no chemotactic activity; instead, it prevented native SDF-1-induced chemotaxis, suggesting that it acted as a potent partial agonist. Our work elucidates the structural basis for sulfotyrosine recognition in the chemokine-receptor interaction and suggests a strategy for CXCR4-targeted drug development.

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Organizational Affiliation: 

Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stromal cell-derived factor 1	A, C	70	Homo sapiens	Mutation(s): 2  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-X-C chemokine receptor type 4	B, D	40	Homo sapiens	Mutation(s): 1  Gene Names: CXCR4
Find proteins for P61073 (Homo sapiens) Explore P61073  Go to UniProtKB:  P61073
NIH Common Fund Data Resources
PHAROS:  P61073 GTEx:  ENSG00000121966

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 
• OLDERADO: 2K04 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-01-24 
• Released Date: 2008-10-28 
Deposition Author(s): Volkman, B.F., Veldkamp, C.T., Peterson, F.C.

Revision History 

• Version 1.0: 2008-10-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-22
  Changes: Database references, Derived calculations
• Version 1.3: 2020-02-19
  Changes: Data collection, Database references, Other