2K03 | pdb_00002k03

Structure of SDF1 in complex with the CXCR4 N-terminus containing a sulfotyrosine at postition 21


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 2K03

This is version 1.6 of the entry. See complete history

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

  • DOI: https://doi.org/10.1126/scisignal.1160755
  • Primary Citation Related Structures: 
    2K01, 2K03, 2K04, 2K05

  • 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.


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

Macromolecule Content 

  • Total Structure Weight: 25.58 kDa 
  • Atom Count: 1,731 
  • Modeled Residue Count: 212 
  • Deposited Residue Count: 220 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Stromal cell-derived factor 1
A, C
70Homo sapiensMutation(s): 2 
Gene Names: CXCL12SDF1SDF1ASDF1B
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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
C-X-C chemokine receptor type 4
B, D
40Homo sapiensMutation(s): 1 
Gene Names: CXCR4
UniProt & NIH Common Fund Data Resources
Find proteins for P61073 (Homo sapiens)
Explore P61073 
Go to UniProtKB:  P61073
PHAROS:  P61073
GTEx:  ENSG00000121966 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61073
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYS
Query on TYS
B, D
L-PEPTIDE LINKINGC9 H11 N O6 STYR

Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-02-19
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.3: 2021-10-20
    Changes: Database references
  • Version 1.4: 2023-06-14
    Changes: Other
  • Version 1.5: 2023-11-15
    Changes: Data collection
  • Version 1.6: 2024-10-09
    Changes: Database references, Structure summary