3J2Q

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


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY

wwPDB Validation   3D Report Full Report



Literature

Domain organization of membrane-bound factor VIII.

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

(2013) Biopolymers 99: 448-459

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

  • 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-b ...

    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.


    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

    Organizational Affiliation

    Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, USA. svmcphie@utmb.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VIII heavy chain A754Homo sapiensMutation(s): 0 
Gene Names: F8F8C
Find proteins for P00451 (Homo sapiens)
Explore P00451 
Go to UniProtKB:  P00451
NIH Common Fund Data Resources
PHAROS:  P00451
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VIII light chain B684Homo sapiensMutation(s): 0 
Gene Names: F8F8C
Find proteins for P00451 (Homo sapiens)
Explore P00451 
Go to UniProtKB:  P00451
NIH Common Fund Data Resources
PHAROS:  P00451
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
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 Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81α = 67
b = 71β = 60
c = 100γ = 65

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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