› 4r9w

X-ray diffraction
2.5Å resolution

Crystal structure of platelet factor 4 complexed with fondaparinux

Released:
DOI: 10.2210/pdb4r9w/pdb
PDB entry 4r9w coloured by chain, front view.
PDB entry 4r9w coloured by chain, side view.
PDB entry 4r9w coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Atomic description of the immune complex involved in heparin-induced thrombocytopenia.
Cai Z, Yarovoi SV, Zhu Z, Rauova L, Hayes V, Lebedeva T, Liu Q, Poncz M, Arepally G, Cines DB, Greene MI
Nat Commun 6 8277 (2015)
PMID: 26391892

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-136202 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Platelet factor 4 Chains: A, B
Molecule details ›
Chains: A, B
Length: 70 amino acids
Theoretical weight: 7.78 KDa
Source organism: Homo sapiens
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: P02776 (Residues: 32-101; Coverage: 100%)
Gene names: CXCL4, PF4, SCYB4
Sequence domains: Small cytokines (intecrine/chemokine), interleukin-8 like
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)

Ligands and Environments

Carbohydrate polymer : NEW Components: ZDO, IDS, SUS, BDP, SGN
Carbohydrate polymer
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4C
Spacegroup: P3221
Unit cell:
a: 67.333Å b: 67.333Å c: 61.756Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.224 0.224 0.245
Expression system: Drosophila melanogaster

Quick links

Citations

21 review citations

Heparin-induced thrombocytopenia.
Arepally GM. (2017)
20 more

13 mentions without citation

Atomic features of an autoantigen in heparin-induced thrombocytopenia (HIT).
Cai et al. (2016)
12 more