Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 17.07 kDa 
• Atom Count: 1081 
• Residue Count: 126 
• Unique protein chains: 1

4R9W

Crystal structure of platelet factor 4 complexed with fondaparinux

• DOI: 10.2210/pdb4R9W/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2014-09-08 Released: 2015-12-16 
• Deposition Author(s): Cai, Z., Zhu, Z., Liu, Q., Greene, M.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.245 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 

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

• PubMed: 26391892 
• DOI: 10.1038/ncomms9277
• Primary Citation of Related Structures:  
  4R97, 4R9W, 4R9Y


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet factor 4	A, B	70	Homo sapiens	Mutation(s): 0  Gene Names: PF4, CXCL4, SCYB4
Find proteins for P02776 (Homo sapiens) Explore P02776  Go to UniProtKB:  P02776
NIH Common Fund Data Resources
PHAROS:  P02776 GTEx:  ENSG00000163737

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside	C	5		N/A

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900028	C	fondaparinux	Oligosaccharide /  Anticoagulant		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.245 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.333	α = 90
b = 67.333	β = 90
c = 61.756	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-09-08 
• Released Date: 2015-12-16 
Deposition Author(s): Cai, Z., Zhu, Z., Liu, Q., Greene, M.I.

Revision History 

• Version 1.0: 2015-12-16
  Type: Initial release
  
• Version 1.1: 2016-01-27
  Changes: Database references
• Version 1.2: 2017-07-12
  Changes: Structure summary
• Version 1.3: 2017-11-22
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary