4CH8

High-salt crystal structure of a thrombin-GpIbalpha peptide complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

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This is version 1.4 of the entry. See complete history. 


Literature

Gpibalpha Interacts Exclusively with Exosite II of Thrombin

Lechtenberg, B.C., Freund, S.M.V., Huntington, J.A.

(2014) J Mol Biol 426: 881

  • DOI: 10.1016/j.jmb.2013.11.027
  • Primary Citation of Related Structures:  
    4CH8, 4CH2

  • PubMed Abstract: 

    • Activation of platelets by the serine protease thrombin is a critical event in haemostasis. This process involves the binding of thrombin to glycoprotein Ibα (GpIbα) and cleavage of protease-activated receptors (PARs). The N-terminal extracellular domain ...

    Activation of platelets by the serine protease thrombin is a critical event in haemostasis. This process involves the binding of thrombin to glycoprotein Ibα (GpIbα) and cleavage of protease-activated receptors (PARs). The N-terminal extracellular domain of GpIbα contains an acidic peptide stretch that has been identified as the main thrombin binding site, and both anion binding exosites of thrombin have been implicated in GpIbα binding, but it remains unclear how they are involved. This issue is of critical importance for the mechanism of platelet activation by thrombin. If both exosites bind to GpIbα, thrombin could potentially act as a platelet adhesion molecule or receptor dimerisation trigger. Alternatively, if only a single site is involved, GpIbα may serve as a cofactor for PAR-1 activation by thrombin. To determine the involvement of thrombin's two exosites in GpIbα binding, we employed the complementary methods of mutational analysis, binding studies, X-ray crystallography and NMR spectroscopy. Our results indicate that the peptide corresponding to the C-terminal portion of GpIbα and the entire extracellular domain bind exclusively to thrombin's exosite II. The interaction of thrombin with GpIbα thus serves to recruit thrombin activity to the platelet surface while leaving exosite I free for PAR-1 recognition.

    Organizational Affiliation: 

    Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, United Kingdom. Electronic address: jah52@cam.ac.uk.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THROMBIN, LIGHT CHAIN A, C, E, G36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734
GTEx:  ENSG00000180210
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
THROMBIN, HEAVY CHAIN B, D, F, H259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734
GTEx:  ENSG00000180210
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300 P, Q, R, S14Homo sapiensMutation(s): 0 
Gene Names: GP1BA
Find proteins for P07359 (Homo sapiens)
Explore P07359 
Go to UniProtKB:  P07359
NIH Common Fund Data Resources
PHAROS:  P07359
GTEx:  ENSG00000185245
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR		P,Q,R,SL-PEPTIDE LINKINGC9 H12 N O6 PTYR
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 5
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000020 (0G6)
Query on PRD_000020		B, D, F, HD-Phe-Pro-Arg-CH2ClPeptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.22α = 90
b = 51.33β = 96.13
c = 150.08γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2013-12-18
    Changes: Database references, Derived calculations, Other
  • Version 1.2: 2013-12-25
    Changes: Non-polymer description
  • Version 1.3: 2014-02-12
    Changes: Database references
  • Version 1.4: 2018-06-27
    Changes: Advisory, Data collection, Structure summary