4C29 | pdb_00004c29

Crystal Structure of High-Affinity von Willebrand Factor A1 domain with Disulfide Mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.235 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4C29

This is version 1.5 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 Biological Chem 289: 5565

  • DOI: https://doi.org/10.1074/jbc.M113.511220
  • Primary Citation Related Structures: 
    4C29, 4C2A, 4C2B

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 50.02 kDa 
  • Atom Count: 3,444 
  • Modeled Residue Count: 402 
  • Deposited Residue Count: 430 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
VON WILLEBRAND FACTOR
A, B
215Homo sapiensMutation(s): 3 
UniProt & NIH Common Fund Data Resources
Find proteins for P04275 (Homo sapiens)
Explore P04275 
Go to UniProtKB:  P04275
PHAROS:  P04275
GTEx:  ENSG00000110799 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04275
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG

Query on PEG



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
H [auth B],
I [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA

Query on CA



Download:Ideal Coordinates CCD File
F [auth A],
G [auth B],
J [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.235 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.249α = 90
b = 50.071β = 92.73
c = 96.869γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-08
    Type: Initial release
  • Version 1.1: 2014-01-15
    Changes: Database references
  • Version 1.2: 2014-01-29
    Changes: Data collection
  • Version 1.3: 2014-03-12
    Changes: Database references
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.5: 2024-11-06
    Changes: Structure summary