4C2B

Crystal Structure of High-Affinity von Willebrand Factor A1 domain with Disulfide Mutation in Complex with High Affinity GPIb alpha

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Towards the Structural Basis of Regulation of Von Willebrand Factor Binding to Glycoprotein Ib

Blenner, M.A., Dong, X., Springer, T.A.

(2014) J.Biol.Chem. 289: 5565

  • DOI: 10.1074/jbc.M113.511220
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Activation by elongational flow of von Willebrand factor (VWF) is critical for primary hemostasis. Mutations causing type 2B von Willebrand disease (VWD), platelet-type VWD (PT-VWD), and tensile force each increase affinity of the VWF A1 domain and p ...

    Activation by elongational flow of von Willebrand factor (VWF) is critical for primary hemostasis. Mutations causing type 2B von Willebrand disease (VWD), platelet-type VWD (PT-VWD), and tensile force each increase affinity of the VWF A1 domain and platelet glycoprotein Ibα (GPIbα) for one another; however, the structural basis for these observations remains elusive. Directed evolution was used to discover a further gain-of-function mutation in A1 that shifts the long range disulfide bond by one residue. We solved multiple crystal structures of this mutant A1 and A1 containing two VWD mutations complexed with GPIbα containing two PT-VWD mutations. We observed a gained interaction between A1 and the central leucine-rich repeats (LRRs) of GPIbα, previously shown to be important at high shear stress, and verified its importance mutationally. These findings suggest that structural changes, including central GPIbα LRR-A1 contact, contribute to VWF affinity regulation. Among the mutant complexes, variation in contacts and poor complementarity between the GPIbα β-finger and the region of A1 harboring VWD mutations lead us to hypothesize that the structures are on a pathway to, but have not yet reached, a force-induced super high affinity state.

    Organizational Affiliation: 

    From the Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VON WILLEBRAND FACTOR
A, C, E, G
215Homo sapiensMutations: Y9C, C10R
Gene Names: VWF (F8VWF)
Find proteins for P04275 (Homo sapiens)
Go to Gene View: VWF
Go to UniProtKB:  P04275
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PLATELET GLYCOPROTEIN IB ALPHA CHAIN
B, D, F, H
291Homo sapiensMutations: N159R, N21R, G233V, M239V
Gene Names: GP1BA
Find proteins for P07359 (Homo sapiens)
Go to Gene View: GP1BA
Go to UniProtKB:  P07359
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PEG
Query on PEG
Download SDF File 
Download CCD File 
G
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES
Download SDF File 
Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.253 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 96.530α = 90.00
b = 103.840β = 90.05
c = 119.930γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-08
    Type: Initial release
  • Version 1.1: 2014-01-15
    Type: Database references
  • Version 1.2: 2014-01-29
    Type: Data collection
  • Version 1.3: 2014-03-12
    Type: Database references, Source and taxonomy