Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 9.60 kDa 
• Atom Count: 752 
• Residue Count: 83 
• Unique protein chains: 1

4BDX

The structure of the FnI-EGF tandem domain of coagulation factor XII

• DOI: 10.2210/pdb4BDX/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2012-10-08 Released: 2013-02-13 
• Deposition Author(s): Beringer, D.X., Kroon-Batenburg, L.M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.247 
• R-Value Work: 0.216 
• R-Value Observed: 0.217 

Literature

The Structure of the Fni-Egf-Like Tandem Domain of Coagulation Factor Xii Solved Using Siras.

Beringer, D.X., Kroon-Batenburg, L.M.J.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 94

• PubMed: 23385745 
• DOI: 10.1107/S1744309113000286
• Primary Citation of Related Structures:  
  4BDW, 4BDX


• PubMed Abstract: 
  

Coagulation factor XII (FXII) is a key protein in the intrinsic coagulation and kallikrein-kinin pathways. It has been found that negative surfaces and amyloids, such as Aβ fibrils, can activate FXII. Additionally, it has been suggested that FXII simulates cells and that it plays an important role in thrombosis. To date, no structural data on FXII have been deposited, which makes it difficult to support any hypothesis on the mechanism of FXII function. The crystal structure of the FnI-EGF-like tandem domain of FXII presented here was solved using experimental phases. To determine the phases, a SIRAS approach was used with a native and a holmium chloride-soaked data set. The holmium cluster was coordinated by the C-terminal tails of two symmetry-related molecules. Another observation was that the FnI domain was much more ordered than the EGF-like domain owing to crystal packing. Furthermore, the structure shows the same domain orientation as the homologous FnI-EGF-like tandem domain of tPA. The plausibility of several proposed interactions of these domains of FXII is discussed. Based on this FXII FnI-EGF-like structure, it could be possible that FXII binding to amyloid and negatively charged surfaces is mediated via this part of FXII.

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Organizational Affiliation: 

Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR XIIA HEAVY CHAIN	A	85	Homo sapiens	Mutation(s): 1  Gene Names: F12 EC: 3.4.21.38
Find proteins for P00748 (Homo sapiens) Explore P00748  Go to UniProtKB:  P00748
NIH Common Fund Data Resources
PHAROS:  P00748 GTEx:  ENSG00000131187

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.247 
• R-Value Work: 0.216 
• R-Value Observed: 0.217 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.788	α = 90
b = 96.788	β = 90
c = 47.477	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-08 
• Released Date: 2013-02-13 
Deposition Author(s): Beringer, D.X., Kroon-Batenburg, L.M.J.

Revision History 

• Version 1.0: 2013-02-13
  Type: Initial release
  
• Version 1.1: 2013-02-20
  Changes: Database references
• Version 1.2: 2013-04-17
  Changes: Other, Structure summary
• Version 1.3: 2016-12-28
  Changes: Database references
• Version 1.4: 2017-07-12
  Changes: Refinement description