3CDZ

Crystal structure of human factor VIII

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.98 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.259 

wwPDB Validation 3D Report Full Report



Literature

Crystal structure of human factor VIII: implications for the formation of the factor IXa-factor VIIIa complex.

Ngo, J.C., Huang, M., Roth, D.A., Furie, B.C., Furie, B.

(2008) Structure 16: 597-606

  • DOI: 10.1016/j.str.2008.03.001
  • Primary Citation of Related Structures:  
    3CDZ

  • PubMed Abstract: 

    • Factor VIII is a procofactor that plays a critical role in blood coagulation, and is missing or defective in hemophilia A. We determined the X-ray crystal structure of B domain-deleted human factor VIII. This protein is composed of five globular doma ...

    Factor VIII is a procofactor that plays a critical role in blood coagulation, and is missing or defective in hemophilia A. We determined the X-ray crystal structure of B domain-deleted human factor VIII. This protein is composed of five globular domains and contains one Ca(2+) and two Cu(2+) ions. The three homologous A domains form a triangular heterotrimer where the A1 and A3 domains serve as the base and interact with the C2 and C1 domains, respectively. The structurally homologous C1 and C2 domains reveal membrane binding features. Based on biochemical studies, a model of the factor IXa-factor VIIIa complex was constructed by in silico docking. Factor IXa wraps across the side of factor VIII, and an extended interface spans the factor VIII heavy and light chains. This model provides insight into the activation of factor VIII and the interaction of factor VIIIa with factor IXa on the membrane surface.

    Organizational Affiliation: 

    Marine Biological Laboratory, Woods Hole, MA 02543, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VIII heavy chainA754Homo sapiensMutation(s): 0 
Gene Names: F8, F8C
Find proteins for P00451 (Homo sapiens)
Explore P00451 
Go to UniProtKB:  P00451
NIH Common Fund Data Resources
PHAROS  P00451
GTEx  ENSG00000185010
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VIII light chainB684Homo sapiensMutation(s): 1 
Gene Names: F8, F8C
Find proteins for P00451 (Homo sapiens)
Explore P00451 
Go to UniProtKB:  P00451
NIH Common Fund Data Resources
PHAROS  P00451
GTEx  ENSG00000185010
Protein Feature View
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 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
4 N/A Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
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B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
CU
Query on CU
Download CCD File 
A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.98 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.259 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.113α = 90
b = 134.113β = 90
c = 349.76γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Advisory, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary