4XZU

Crystal Structure of the Human Factor VIII C2 Domain in Complex with Murine 3E6 Inhibitory Antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Human Factor VIII C2 Domain in Complex with the 3E6 Inhibitory Antibody.

Wuerth, M.E.Cragerud, R.K.Clint Spiegel, P.

(2015) Sci Rep 5: 17216-17216

  • DOI: 10.1038/srep17216

  • PubMed Abstract: 
  • Blood coagulation factor VIII is a glycoprotein cofactor that is essential for the intrinsic pathway of the blood coagulation cascade. Inhibitory antibodies arise either spontaneously or in response to therapeutic infusion of functional factor VIII i ...

    Blood coagulation factor VIII is a glycoprotein cofactor that is essential for the intrinsic pathway of the blood coagulation cascade. Inhibitory antibodies arise either spontaneously or in response to therapeutic infusion of functional factor VIII into hemophilia A patients, many of which are specific to the factor VIII C2 domain. The immune response is largely parsed into "classical" and "non-classical" inhibitory antibodies, which bind to opposing faces cooperatively. In this study, the 2.61 Å resolution structure of the C2 domain in complex with the antigen-binding fragment of the 3E6 classical inhibitory antibody is reported. The binding interface is largely conserved when aligned with the previously determined structure of the C2 domain in complex with two antibodies simultaneously. Further inspection of the B factors for the C2 domain in various X-ray crystal structures indicates that 3E6 antibody binding decreases the thermal motion behavior of surface loops in the C2 domain on the opposing face, thereby suggesting that cooperative antibody binding is a dynamic effect. Understanding the structural nature of the immune response to factor VIII following hemophilia A treatment will help lead to the development of better therapeutic reagents.


    Related Citations: 
    • Crystal structure of the human factor VIII C2 domain in complex with the 3E6 inhibitory antibody at 2.6 Angstroms resolution
      Wuerth, M.E.,Spiegel, P.C.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Western Washington University, Department of Chemistry, 516 High Street, Bellingham, WA 98225-9150.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3E6 antibody Fab heavy chain
A, E
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
3E6 antibody Fab light chain
B, F
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor VIII
M, G
154Homo sapiensMutation(s): 0 
Gene Names: F8 (F8C)
Find proteins for P00451 (Homo sapiens)
Go to Gene View: F8
Go to UniProtKB:  P00451
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, F, M
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.199 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.229α = 90.00
b = 148.492β = 90.00
c = 188.417γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data scaling
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood InstituteUnited StatesR15HL103518-01

Revision History 

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2015-12-16
    Type: Derived calculations
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Derived calculations