Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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: 167.25 kDa 
• Atom Count: 10317 
• Modelled Residue Count: 1261 
• Deposited Residue Count: 1438 
• Unique protein chains: 2

3CDZ

Crystal structure of human factor VIII

• PDB DOI: 10.2210/pdb3CDZ/pdb

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


• 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 
• R-Value Observed: 0.259 

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
• 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 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VIII heavy chain	A	754	Homo sapiens	Mutation(s): 0  Gene Names: F8, F8C
UniProt & NIH Common Fund Data Resources
Find proteins for P00451 (Homo sapiens) Explore P00451  Go to UniProtKB:  P00451
PHAROS:  P00451 GTEx:  ENSG00000185010

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VIII light chain	B	684	Homo sapiens	Mutation(s): 1  Gene Names: F8, F8C
UniProt & NIH Common Fund Data Resources
Find proteins for P00451 (Homo sapiens) Explore P00451  Go to UniProtKB:  P00451
PHAROS:  P00451 GTEx:  ENSG00000185010

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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
Glycosylation Resources
GlyTouCan:  G95760DN GlyCosmos:  G95760DN GlyGen:  G95760DN

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth B], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CU	E [auth A], I [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 134.113	α = 90
b = 134.113	β = 90
c = 349.76	γ = 90

Software Package:

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

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
  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