Biological Assembly 1  

 3D View: Structure

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - ABCD Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer -A2BC 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 83531.41 
• Atom Count: 5864 
• Residue Count: 731 
• Unique protein chains: 4

1U0N

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

• DOI: 10.2210/pdb1U0N/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Bothrops jararaca, Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): 2 


• Deposited: 2004-07-13 Released: 2005-04-19 
• Deposition Author(s): Fukuda, K., Liddington, R.C.

---

Experimental Data Snapshot

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

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

• PubMed: 15665869 
• DOI: 10.1038/nsmb892
• Primary Citation of Related Structures:  
  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. 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
Molecule	Chains	Sequence Length	Organism	Details
Von Willebrand factor	A	208	Homo sapiens	Mutation(s): 0  Gene Names: VWF (F8VWF)
Find proteins for P04275 (Homo sapiens) Go to Gene View: VWF Go to UniProtKB:  P04275

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Botrocetin	B	133	Bothrops jararaca	Mutation(s): 0
Find proteins for P22029 (Bothrops jararaca) Go to UniProtKB:  P22029

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Botrocetin	C	125	Bothrops jararaca	Mutation(s): 0
Find proteins for P22030 (Bothrops jararaca) Go to UniProtKB:  P22030

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Platelet glycoprotein Ib	D	265	Homo sapiens	Mutation(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 = 108.315	α = 90.00
b = 108.315	β = 90.00
c = 221.967	γ = 90.00

Software Package:

Software Name	Purpose
AMoRE	phasing
DENZO	data reduction
CNS	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-07-13 
• Released Date: 2005-04-19 
• Deposition Author(s): Fukuda, K., Liddington, R.C.

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