Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 176.52 kDa 
• Atom Count: 10985 
• Residue Count: 1337 
• Unique protein chains: 2

2R7E

Crystal Structure Analysis of Coagulation Factor VIII

• DOI: 10.2210/pdb2R7E/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2007-09-07 Released: 2008-04-15 
• Deposition Author(s): Stoddard, B.L., Shen, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 0.347 
• R-Value Work: 0.279 
• R-Value Observed: 0.279 

Literature

The tertiary structure and domain organization of coagulation factor VIII.

Shen, B.W., Spiegel, P.C., Chang, C.H., Huh, J.W., Lee, J.S., Kim, J., Kim, Y.H., Stoddard, B.L.

(2008) Blood 111: 1240-1247

• PubMed: 17965321 
• DOI: 10.1182/blood-2007-08-109918
• Primary Citation of Related Structures:  
  2R7E


• PubMed Abstract: 
  

Factor VIII (fVIII) is a serum protein in the coagulation cascade that nucleates the assembly of a membrane-bound protease complex on the surface of activated platelets at the site of a vascular injury. Hemophilia A is caused by a variety of mutations in the factor VIII gene and typically requires replacement therapy with purified protein. We have determined the structure of a fully active, recombinant form of factor VIII (r-fVIII), which consists of a heterodimer of peptides, respectively containing the A1-A2 and A3-C1-C2 domains. The structure permits unambiguous modeling of the relative orientations of the 5 domains of r-fVIII. Comparison of the structures of fVIII, fV, and ceruloplasmin indicates that the location of bound metal ions and of glycosylation, both of which are critical for domain stabilization and association, overlap at some positions but have diverged at others.

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Organizational Affiliation: 

Program in Molecular Biophysics, Structure and Design, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VIII	A	742	Homo sapiens	Mutation(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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VIII	B	770	Homo sapiens	Mutation(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

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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	4		N-Glycosylation

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-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	E	7		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	A, B	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 0.347 
• R-Value Work: 0.279 
• R-Value Observed: 0.279 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.569	α = 90
b = 134.569	β = 90
c = 359.496	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-09-07 
• Released Date: 2008-04-15 
Deposition Author(s): Stoddard, B.L., Shen, B.W.

Revision History 

• Version 1.0: 2008-04-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary