4R9W

Crystal structure of platelet factor 4 complexed with fondaparinux


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Atomic description of the immune complex involved in heparin-induced thrombocytopenia.

Cai, Z.Yarovoi, S.V.Zhu, Z.Rauova, L.Hayes, V.Lebedeva, T.Liu, Q.Poncz, M.Arepally, G.Cines, D.B.Greene, M.I.

(2015) Nat Commun 6: 8277-8277

  • DOI: 10.1038/ncomms9277
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Heparin-induced thrombocytopenia (HIT) is an autoimmune thrombotic disorder caused by immune complexes containing platelet factor 4 (PF4), antibodies to PF4 and heparin or cellular glycosaminoglycans (GAGs). Here we solve the crystal structures of th ...

    Heparin-induced thrombocytopenia (HIT) is an autoimmune thrombotic disorder caused by immune complexes containing platelet factor 4 (PF4), antibodies to PF4 and heparin or cellular glycosaminoglycans (GAGs). Here we solve the crystal structures of the: (1) PF4 tetramer/fondaparinux complex, (2) PF4 tetramer/KKO-Fab complex (a murine monoclonal HIT-like antibody) and (3) PF4 monomer/RTO-Fab complex (a non-HIT anti-PF4 monoclonal antibody). Fondaparinux binds to the 'closed' end of the PF4 tetramer and stabilizes its conformation. This interaction in turn stabilizes the epitope for KKO on the 'open' end of the tetramer. Fondaparinux and KKO thereby collaborate to 'stabilize' the ternary pathogenic immune complex. Binding of RTO to PF4 monomers prevents PF4 tetramerization and inhibits KKO and human HIT IgG-induced platelet activation and platelet aggregation in vitro, and thrombus progression in vivo. The atomic structures provide a basis to develop new diagnostics and non-anticoagulant therapeutics for HIT.


    Organizational Affiliation

    Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Platelet factor 4
A, B
70Homo sapiensMutation(s): 0 
Gene Names: PF4 (CXCL4, SCYB4)
Find proteins for P02776 (Homo sapiens)
Go to Gene View: PF4
Go to UniProtKB:  P02776
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NTO
Query on NTO

Download SDF File 
Download CCD File 
B
TRISULFOAMINO HEPARIN PENTASACCHARIDE
Fondaparinux
C31 H53 N3 O49 S8
KANJSNBRCNMZMV-ABRZTLGGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.224 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 67.333α = 90.00
b = 67.333β = 90.00
c = 61.756γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-01-27
    Type: Database references
  • Version 1.2: 2017-07-12
    Type: Structure summary
  • Version 1.3: 2017-11-22
    Type: Refinement description