9D5D | pdb_00009d5d

Crystal Structure of Blood Coagulation Factor VIII C2 Domain Mutant L2251A/L2252A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 
    0.223 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Biophysical characterization of blood coagulation factor VIII binding to lipid nanodiscs that mimic activated platelet surfaces.

Avery, N.G.Young, I.R.Lu, S.Vaughan, J.D.Korus, P.S.Richardson, T.N.Childers, K.C.Smirnov, S.L.Spiegel Jr., P.C.

(2024) J Thromb Haemost 

  • DOI: https://doi.org/10.1016/j.jtha.2024.11.003
  • Primary Citation Related Structures: 
    9D5D

  • PubMed Abstract: 

    Following proteolytic activation, activated blood coagulation factor (F)VIII (FVIIIa) binds to activated platelet membranes, forming the intrinsic tenase complex with activated FIX (FIXa). Previous studies have identified the C1 and C2 domains as the membrane binding domains of FVIII through conserved arginine residues. A membrane binding model for the FVIII C domains proposes that surface-exposed hydrophobic and positively charged residues at each C domain interact with the membrane, yet a comprehensive thermodynamic and structural description of this interaction is lacking. To determine residues of interaction, thermodynamics, and membrane binding preference for FVIII membrane association. The binding of FVIII constructs to lipid nanodiscs was characterized by nuclear magnetic resonance, isothermal titration calorimetry, bio-layer interferometry, and X-ray crystallography. The thermodynamics of FVIII membrane binding indicated that the C1 domain associates through an enthalpically driven process while the C2 domain is entropically driven. Alanine mutations to surface-exposed hydrophobic residues in the C2 domain revealed differential effects on membrane binding, highlighting important determinants at the residue level. The structure of a C2 double mutant, L2251A/L2252A, demonstrated that its decreased affinity is likely due to decreasing the surface area hydrophobicity. Nuclear magnetic resonance studies with the C2 domain identified residues of interaction with soluble O-phospho-L-serine as well as lipid nanodiscs. Lastly, increasing phosphatidylethanolamine and decreasing phosphatidylserine content decreased overall FVIII affinity for membrane surfaces. This study provides further insight into the molecular basis for how FVIII interacts with platelets to form the intrinsic tenase complex.


  • Organizational Affiliation
    • Chemistry Department, Western Washington University, Bellingham, Washington, USA.

Macromolecule Content 

  • Total Structure Weight: 18.56 kDa 
  • Atom Count: 1,409 
  • Modeled Residue Count: 158 
  • Deposited Residue Count: 164 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Factor VIIIa light chainA [auth M]164Homo sapiensMutation(s): 2 
Gene Names: F8F8C
UniProt & NIH Common Fund Data Resources
Find proteins for P00451 (Homo sapiens)
Explore P00451 
Go to UniProtKB:  P00451
PHAROS:  P00451
GTEx:  ENSG00000185010 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00451
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free:  0.223 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.962α = 90
b = 49.962β = 90
c = 116.565γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHENIXphasing
APEXdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR15 HL135658
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesU54 HL141981

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Structure summary
  • Version 1.2: 2024-12-18
    Changes: Database references