Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 167320.02 
• Atom Count: 10317 
• Residue Count: 1438 
• Unique protein chains: 2

3CDZ

Crystal structure of human factor VIII

• DOI: 10.2210/pdb3CDZ/pdb

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


• Deposited: 2008-02-27 Released: 2008-04-01 
• Deposition Author(s): Ngo, J.C., Huang, M., Roth, D.A., Furie, B.C., Furie, B.

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Experimental Data Snapshot

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

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

• PubMed: 18400180 
• DOI: 10.1016/j.str.2008.03.001


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Coagulation factor VIII heavy chain	A	754	Homo sapiens	Mutation(s): 0  Gene Names: F8 (F8C)
Find proteins for P00451 (Homo sapiens) Go to Gene View: F8 Go to UniProtKB:  P00451

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Coagulation factor VIII light chain	B	684	Homo sapiens	Mutation(s): 0  Gene Names: F8 (F8C)
Find proteins for P00451 (Homo sapiens) Go to Gene View: F8 Go to UniProtKB:  P00451

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MAN	B	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
CU	A, B	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
NAG	A, B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.98 Å
• R-Value Free: 0.327 
• R-Value Work: 0.256 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 134.113	α = 90.00
b = 134.113	β = 90.00
c = 349.760	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data scaling
DENZO	data reduction
HKL-2000	data reduction
AMoRE	phasing
PDB_EXTRACT	data extraction
REFMAC	refinement
SCALEPACK	data scaling
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-02-27 
• Released Date: 2008-04-01 
• Deposition Author(s): Ngo, J.C., Huang, M., Roth, D.A., Furie, B.C., Furie, B.

Revision History 

• Version 1.0: 2008-04-01
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Type: Advisory, Refinement description