1PLF

THE THREE-DIMENSIONAL STRUCTURE OF BOVINE PLATELET FACTOR 4 AT 3.0 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The three-dimensional structure of bovine platelet factor 4 at 3.0-A resolution.

St Charles, R.Walz, D.A.Edwards, B.F.

(1989) J Biol Chem 264: 2092-2099

  • Primary Citation of Related Structures:  
    1PLF

  • PubMed Abstract: 
  • Platelet factor 4 (PF4), which is released by platelets during coagulation, binds very tightly to negatively charged oligosaccharides such as heparin. To date, six other proteins are known that are homologous in sequence with PF4 but have quite different functions ...

    Platelet factor 4 (PF4), which is released by platelets during coagulation, binds very tightly to negatively charged oligosaccharides such as heparin. To date, six other proteins are known that are homologous in sequence with PF4 but have quite different functions. The structure of a tetramer of bovine PF4 complexed with one Ni(CN)4(2-) molecule has been determined at 3.0 A resolution and refined to an R factor of 0.28. The current model contains residues 24-85, no solvent, and one overall temperature factor. Residues 1-13, which carried an oligosaccharide chain, were removed with elastase to induce crystallization; residues 14-23 and presumably 86-88 are disordered in the electron density map. Because no heavy atom derivative was isomorphous with the native crystals, the complex of PF4 with one Ni(CN)4(2-) molecule was solved using a single, highly isomorphous Pt(CN)4(2-) derivative and the iterative, single isomorphous replacement method. The secondary structure of the PF4 subunit, from amino- to carboxyl-terminal end, consists of an extended loop, three strands of antiparallel beta-sheet arranged in a Greek key, and one alpha-helix. The tetramer contains two extended, six-stranded beta-sheets, each formed by two subunits, which are arranged back-to-back to form a "beta-bilayer" structure with two buried salt bridges sandwiched in the middle. The carboxyl-terminal alpha-helices, which contain lysine residues that are thought to be intimately involved in binding heparin, are arranged as antiparallel pairs on the surface of each extended beta-sheet.


    Related Citations: 
    • X-Ray Diffraction Analysis of Crystals of Bovine Platelet Factor 4
      Charles, R.St., Ciaglowski, R.E., Walz, D., Edwards, B.F.P.
      (1984) J Mol Biol 176: 421

    Organizational Affiliation

    Department of Biochemistry, Wayne State University School of Medicine, Detroit, Michigan 48201.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PLATELET FACTOR 4A, B, C, D72Bos taurusMutation(s): 0 
Gene Names: PF4CXCL4SCYB4
UniProt
Find proteins for P02777 (Bos taurus)
Explore P02777 
Go to UniProtKB:  P02777
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TCN
Query on TCN

Download Ideal Coordinates CCD File 
E [auth D]TETRACYANONICKELATE ION
C4 N4 Ni
FUWOSUXMFKRUSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.7α = 90
b = 68β = 90
c = 80.3γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-17
    Changes: Data collection, Other, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection, Refinement description