Biological Assembly 1  

 3D View: Structure

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 166.49 kDa 
• Atom Count: 11928 
• Residue Count: 1420 
• Unique protein chains: 1

1FIE

RECOMBINANT HUMAN COAGULATION FACTOR XIII

• DOI: 10.2210/pdb1FIE/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 1996-08-24 Released: 1997-02-12 
• Deposition Author(s): Yee, V.C., Teller, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.182 
• R-Value Observed: 0.182 

Literature

Structural evidence that the activation peptide is not released upon thrombin cleavage of factor XIII.

Yee, V.C., Pedersen, L.C., Bishop, P.D., Stenkamp, R.E., Teller, D.C.

(1995) Thromb Res 78: 389-397

• PubMed: 7660355 
• DOI: 10.1016/0049-3848(95)00072-y
• Primary Citation of Related Structures:  
  1FIE


• PubMed Abstract: 
  

The three-dimensional structure of the recombinant human factor XIII a2 dimer after cleavage by thrombin has been determined by X-ray crystallography. Factor XIII zymogen was treated with bovine alpha-thrombin in the presence of 3 mM CaCl2, and the cleaved protein was crystallized from Tris buffered at pH 6.5 using ethanol as the precipitating agent. Refinement of the molecular model of thrombin-cleaved factor XIII against diffraction data from 10.0 to 2.5 A resolution has been carried out to give a crystallographic R factor of 18.2%. The structure of thrombin-cleaved factor XIII is remarkably similar to that of the zymogen: there are no large conformational changes in the protein and the 37 residue amino terminus activation peptide remains associated with the rest of the molecule. This work shows that the activation peptide, upon thrombin cleavage, has the same conformation and occupies the same position with respect to the rest of the molecule as it does in the zymogen structure.

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Related Citations: 

• Transglutaminase Factor Xiii Uses Proteinase-Like Catalytic Triad to Crosslink Macromolecules
  Pedersen, L.C., Yee, V.C., Bishop, P.D., Le Trong, I., Teller, D.C., Stenkamp, R.E.
  (1994) Protein Sci 3: 1131

• Three-Dimensional Structure of a Transglutaminase: Human Blood Coagulation Factor Xiii
  Yee, V.C., Pedersen, L.C., Le Trong, I., Bishop, P.D., Stenkamp, R.E., Teller, D.C.
  (1994) Proc Natl Acad Sci U S A 91: 7296

• Expression, Purification, and Characterization of Human Factor Xiii in Saccharomyces Cerevisiae
  Bishop, P.D., Teller, D.C., Smith, R.A., Lasser, G.W., Gilbert, T., Seale, R.L.
  (1990) Biochemistry 29: 1861

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Organizational Affiliation: 

Department of Biochemistry, University of Washington, Seattle 98195, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR XIII	A, B	731	Homo sapiens	Mutation(s): 0  Gene Names: F13A1, F13A EC: 2.3.2.13
Find proteins for P00488 (Homo sapiens) Explore P00488  Go to UniProtKB:  P00488
NIH Common Fund Data Resources
PHAROS:  P00488 GTEx:  ENSG00000124491

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.182 
• R-Value Observed: 0.182 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.1	α = 90
b = 73.13	β = 106.4
c = 134.7	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
R-AXIS	data reduction
R-AXIS	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-08-24 
• Released Date: 1997-02-12 
Deposition Author(s): Yee, V.C., Teller, D.C.

Revision History 

• Version 1.0: 1997-02-12
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance