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Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-alpha at 2.8 Angstrom Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Platinum-induced space-group transformation in crystals of the platelet glycoprotein Ib alpha N-terminal domain.

Varughese, K.I.Ruggeri, Z.M.Celikel, R.

(2004) Acta Crystallogr.,Sect.D 60: 405-411

  • DOI: 10.1107/S0907444903026805

  • PubMed Abstract: 
  • The interaction between platelet glycoprotein (GP) Ib alpha and von Willebrand factor (VWF) is essential for thrombus formation, leading to the arrest of bleeding. The N-terminal domain of GP Ib alpha, which contains the binding sites for VWF and alp ...

    The interaction between platelet glycoprotein (GP) Ib alpha and von Willebrand factor (VWF) is essential for thrombus formation, leading to the arrest of bleeding. The N-terminal domain of GP Ib alpha, which contains the binding sites for VWF and alpha-thrombin, crystallized in the tetragonal space group P4(3) with one molecule in the asymmetric unit. When the crystals were treated with platinum, the crystals changed their symmetry from tetragonal to monoclinic P2(1) with two molecules in the asymmetric unit. The structure of the monoclinic form was solved using two-wavelength platinum anomalous dispersion data. The tetragonal crystal structure was subsequently solved using molecular-replacement techniques using the monoclinic structure as the search model and was refined with 1.7 A resolution data.


    Organizational Affiliation

    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA. kiv@scripps.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Platelet glycoprotein Ib alpha chain
A, G
290Homo sapiensMutation(s): 1 
Gene Names: GP1BA
Find proteins for P07359 (Homo sapiens)
Go to Gene View: GP1BA
Go to UniProtKB:  P07359
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PT
Query on PT

Download SDF File 
Download CCD File 
A, G
PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.610α = 90.00
b = 113.820β = 95.21
c = 56.210γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALEPACKdata scaling
CNSrefinement
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-02
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance