3PPV

Crystal structure of an engineered VWF A2 domain (N1493C and C1670S)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A novel calcium-binding site of von Willebrand factor A2 domain regulates its cleavage by ADAMTS13

Zhou, M.Dong, X.Baldauf, C.Chen, H.Zhou, Y.Springer, T.A.Luo, X.Zhong, C.Grater, F.Ding, J.

(2011) Blood 117: 4623-4631

  • DOI: 10.1182/blood-2010-11-321596
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The proteolysis of VWF by ADAMTS13 is an essential step in the regulation of its hemostatic and thrombogenic potential. The cleavage occurs at strand β4 in the structural core of the A2 domain of VWF, so unfolding of the A2 domain is a prerequisite f ...

    The proteolysis of VWF by ADAMTS13 is an essential step in the regulation of its hemostatic and thrombogenic potential. The cleavage occurs at strand β4 in the structural core of the A2 domain of VWF, so unfolding of the A2 domain is a prerequisite for cleavage. In the present study, we present the crystal structure of an engineered A2 domain that exhibits a significant difference in the α3-β4 loop compared with the previously reported structure of wild-type A2. Intriguingly, a metal ion was detected at a site formed mainly by the C-terminal region of the α3-β4 loop that was later identified as Ca(²+) after various biophysical and biochemical studies. Force-probe molecular dynamic simulations of a modeled structure of the wild-type A2 featuring the discovered Ca(²+)-binding site revealed that an increase in force was needed to unfold strand β4 when Ca(²+) was bound. Cleavage assays consistently demonstrated that Ca(²+) binding stabilized the A2 domain and impeded its unfolding, and consequently protected it from cleavage by ADAMTS13. We have revealed a novel Ca(²+)-binding site at the A2 domain of VWF and demonstrated a relationship between Ca(²+) and force in the regulation of VWF and primary hemostasis.


    Organizational Affiliation

    State Key Laboratory of Molecular Biology and Research Center for Structural Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
von Willebrand factor
A
196Homo sapiensMutation(s): 2 
Gene Names: VWF (F8VWF)
Find proteins for P04275 (Homo sapiens)
Go to Gene View: VWF
Go to UniProtKB:  P04275
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.202 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 69.759α = 90.00
b = 69.759β = 90.00
c = 73.605γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement
PHASERphasing
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-03-05
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description