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 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    1U0N, 1U0O

  • 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 kinetic and crystallographic analysis of this interaction that reveals a novel mechanism of affinity enhancement ...

    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 factorA208Homo sapiensMutation(s): 0 
Gene Names: VWFF8VWF
UniProt & NIH Common Fund Data Resources
Find proteins for P04275 (Homo sapiens)
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Go to UniProtKB:  P04275
PHAROS:  P04275
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BotrocetinB133Bothrops jararacaMutation(s): 0 
UniProt
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
BotrocetinC125Bothrops jararacaMutation(s): 0 
UniProt
Find proteins for P22030 (Bothrops jararaca)
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Go to UniProtKB:  P22030
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Platelet glycoprotein IbD265Homo sapiensMutation(s): 2 
Gene Names: GP1BA
UniProt & NIH Common Fund Data Resources
Find proteins for P07359 (Homo sapiens)
Explore P07359 
Go to UniProtKB:  P07359
PHAROS:  P07359
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  (Full details and data files)

  • 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
  • Version 1.3: 2021-10-27
    Changes: Database references