4BDX

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

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 69: 94

  • DOI: 10.1107/S1744309113000286
  • Primary Citation of Related Structures:  

  • 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 sim ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COAGULATION FACTOR XIIA HEAVY CHAIN
A
85Homo sapiensMutation(s): 0 
Gene Names: F12
EC: 3.4.21.38
Find proteins for P00748 (Homo sapiens)
Go to Gene View: F12
Go to UniProtKB:  P00748
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.216 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 96.788α = 90.00
b = 96.788β = 90.00
c = 47.477γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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