6MF0

Crystal Structure Determination of Human/Porcine Chimera Coagulation Factor VIII


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report

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This is version 2.1 of the entry. See complete history


Literature

The 3.2 angstrom structure of a bioengineered variant of blood coagulation factor VIII indicates two conformations of the C2 domain.

Smith, I.W.d'Aquino, A.E.Coyle, C.W.Fedanov, A.Parker, E.T.Denning, G.Spencer, H.T.Lollar, P.Doering, C.B.Spiegel Jr., P.C.

(2020) J Thromb Haemost 18: 57-69

  • DOI: https://doi.org/10.1111/jth.14621
  • Primary Citation of Related Structures:  
    6MF0, 6MF2

  • PubMed Abstract: 

    Coagulation factor VIII represents one of the oldest protein-based therapeutics, serving as an effective hemophilia A treatment for half a century. Optimal treatment consists of repeated intravenous infusions of blood coagulation factor VIII (FVIII) per week for life. Despite overall treatment success, significant limitations remain, including treatment invasiveness, duration, immunogenicity, and cost. These issues have inspired research into the development of bioengineered FVIII products and gene therapies.


  • Organizational Affiliation

    Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Emory University, Atlanta, Georgia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor VIII chimera
A, B
1,467Sus scrofaHomo sapiensMutation(s): 0 
Gene Names: F8CF8F8C
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P12263 (Sus scrofa)
Explore P12263 
Go to UniProtKB:  P12263
Find proteins for P00451 (Homo sapiens)
Explore P00451 
Go to UniProtKB:  P00451
GTEx:  ENSG00000185010 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP12263P00451
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, E, F
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
G
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G35459KZ
GlyCosmos:  G35459KZ
GlyGen:  G35459KZ
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.005α = 90
b = 135.863β = 90.151
c = 196.107γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Currently 6MF0 does not have a validation slider image.



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR15 HL103518
National Science Foundation (NSF, United States)United StatesMRI 1429164

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2020-01-15
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary