Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction | Predict Membrane 

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 167.25 kDa 
• Atom Count: 10317 
• Modelled Residue Count: 1261 
• Deposited Residue Count: 1438 
• Unique protein chains: 2

3J2Q

Model of membrane-bound factor VIII organized in 2D crystals

• PDB DOI: 10.2210/pdb3J2Q/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2012-12-11 Released: 2013-09-11 
• Deposition Author(s): Stoilova-Mcphie, S., Lynch, G.C., Ludtke, S., Pettitt, B.M.

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY

Literature

Domain organization of membrane-bound factor VIII.

Stoilova-McPhie, S., Lynch, G.C., Ludtke, S., Pettitt, B.M.

(2013) Biopolymers 99: 448-459

• PubMed: 23616213 
• DOI: 10.1002/bip.22199
• Primary Citation of Related Structures:  
  3J2Q, 3J2S


• PubMed Abstract: 
  

Factor VIII (FVIII) is the blood coagulation protein which when defective or deficient causes for hemophilia A, a severe hereditary bleeding disorder. Activated FVIII (FVIIIa) is the cofactor to the serine protease factor IXa (FIXa) within the membrane-bound Tenase complex, responsible for amplifying its proteolytic activity more than 100,000 times, necessary for normal clot formation. FVIII is composed of two noncovalently linked peptide chains: a light chain (LC) holding the membrane interaction sites and a heavy chain (HC) holding the main FIXa interaction sites. The interplay between the light and heavy chains (HCs) in the membrane-bound state is critical for the biological efficiency of FVIII. Here, we present our cryo-electron microscopy (EM) and structure analysis studies of human FVIII-LC, when helically assembled onto negatively charged single lipid bilayer nanotubes. The resolved FVIII-LC membrane-bound structure supports aspects of our previously proposed FVIII structure from membrane-bound two-dimensional (2D) crystals, such as only the C2 domain interacts directly with the membrane. The LC is oriented differently in the FVIII membrane-bound helical and 2D crystal structures based on EM data, and the existing X-ray structures. This flexibility of the FVIII-LC domain organization in different states is discussed in the light of the FVIIIa-FIXa complex assembly and function.

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Related Citations: 

• 3-Dimensional structure of membrane-bound coagulation factor VIII: modeling of the factor VIII heterodimer within a 3-dimensional density map derived by electron crystallography.
  Stoilova-McPhie, S., Villoutreix, B.O., Mertens, K., Kemball-Cook, G., Holzenburg, A.
  (2002) Blood 99: 1215

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Organizational Affiliation: 

Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, USA. [e-mail]

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 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P00451 (Homo sapiens) Explore P00451  Go to UniProtKB:  P00451
PHAROS:  P00451

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VIII light chain	B	684	Homo sapiens	Mutation(s): 0  Gene Names: F8, F8C Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P00451 (Homo sapiens) Explore P00451  Go to UniProtKB:  P00451
PHAROS:  P00451

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)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	4		N/A
Glycosylation Resources
GlyTouCan:  G11348GW GlyCosmos:  G11348GW GlyGen:  G11348GW

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: ELECTRON CRYSTALLOGRAPHY
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81	α = 67
b = 71	β = 60
c = 100	γ = 65

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-12-11 
• Released Date: 2013-09-11 
Deposition Author(s): Stoilova-Mcphie, S., Lynch, G.C., Ludtke, S., Pettitt, B.M.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Structure summary