1U0N

The ternary von Willebrand Factor A1-glycoprotein Ibalpha-botrocetin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The snake venom protein botrocetin acts as a biological brace to promote dysfunctional platelet aggregation

Fukuda, K.Doggett, T.Laurenzi, I.J.Liddington, R.C.Diacovo, T.G.

(2005) Nat.Struct.Mol.Biol. 12: 152-159

  • DOI: 10.1038/nsmb892
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Botrocetin is a snake venom protein that enhances the affinity of the A1 domain of plasma von Willebrand factor (vWF) for the platelet receptor glycoprotein Ibalpha (GPIbalpha), an event that contributes to bleeding and host death. Here we describe a ...

    Botrocetin is a snake venom protein that enhances the affinity of the A1 domain of plasma von Willebrand factor (vWF) for the platelet receptor glycoprotein Ibalpha (GPIbalpha), an event that contributes to bleeding and host death. Here we describe a kinetic and crystallographic analysis of this interaction that reveals a novel mechanism of affinity enhancement. Using high-temporal-resolution microscopy, we show that botrocetin decreases the GPIbalpha off-rate two-fold in both human and mouse complexes without affecting the on-rate. The key to this behavior is that, upon binding of GPIbalpha to vWF-A1, botrocetin prebound to vWF-A1 makes no contacts initially with GPIbalpha, but subsequently slides around the A1 surface to form a new interface. This two-step mechanism and flexible coupling may prevent adverse alterations in on-rate of GPIbalpha for vWF-A1, and permit adaptation to structural differences in GPIbalpha and vWF in several prey species.


    Organizational Affiliation

    Infectious and Inflammatory Disease Center, The Burnham Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Von Willebrand factor
A
208Homo sapiensMutation(s): 0 
Gene Names: VWF (F8VWF)
Find proteins for P04275 (Homo sapiens)
Go to Gene View: VWF
Go to UniProtKB:  P04275
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Botrocetin
B
133Bothrops jararacaMutation(s): 0 
Find proteins for P22029 (Bothrops jararaca)
Go to UniProtKB:  P22029
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Botrocetin
C
125Bothrops jararacaMutation(s): 0 
Find proteins for P22030 (Bothrops jararaca)
Go to UniProtKB:  P22030
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Platelet glycoprotein Ib
D
265Homo sapiensMutation(s): 2 
Gene Names: GP1BA
Find proteins for P07359 (Homo sapiens)
Go to Gene View: GP1BA
Go to UniProtKB:  P07359
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.213 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 108.315α = 90.00
b = 108.315β = 90.00
c = 221.967γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance