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 
  • R-Value Observed: 0.213 

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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:  
    1U0O, 1U0N

  • 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 kin ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Von Willebrand factor A208Homo sapiensMutation(s): 0 
Gene Names: VWF, F8VWF
Find proteins for P04275 (Homo sapiens)
Explore P04275 
Go to UniProtKB:  P04275
NIH Common Fund Data Resources
PHAROS:  P04275
GTEx:  ENSG00000110799
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Botrocetin B133Bothrops jararacaMutation(s): 0 
Find proteins for P22029 (Bothrops jararaca)
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Go to UniProtKB:  P22029
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Botrocetin C125Bothrops jararacaMutation(s): 0 
Find proteins for P22030 (Bothrops jararaca)
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Go to UniProtKB:  P22030
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Platelet glycoprotein Ib D265Homo sapiensMutation(s): 2 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.315α = 90
b = 108.315β = 90
c = 221.967γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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