3T1W

Structure of the four-domain fragment Fn7B89 of oncofetal fibronectin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Extra-domain B in oncofetal fibronectin structurally promotes fibrillar head-to-tail dimerization of extracellular matrix protein.

Schiefner, A.Gebauer, M.Skerra, A.

(2012) J.Biol.Chem. 287: 17578-17588

  • DOI: 10.1074/jbc.M111.303131

  • PubMed Abstract: 
  • The type III extra-domain B (ED-B) is specifically spliced into fibronectin (Fn) during embryogenesis and neoangiogenesis, including many cancers. The x-ray structure of the recombinant four-domain fragment Fn(III)7B89 reveals a tightly associated, e ...

    The type III extra-domain B (ED-B) is specifically spliced into fibronectin (Fn) during embryogenesis and neoangiogenesis, including many cancers. The x-ray structure of the recombinant four-domain fragment Fn(III)7B89 reveals a tightly associated, extended head-to-tail dimer, which is stabilized via pair-wise shape and charge complementarity. A tendency toward ED-B-dependent dimer formation in solution was supported by size exclusion chromatography and analytical ultracentrifugation. When amending the model with the known three-dimensional structure of the Fn(III)10 domain, its RGD loop as well as the adhesion synergy region in Fn(III)9-10 become displayed on the same face of the dimer; this should allow simultaneous binding of at least two integrins and, thus, receptor clustering on the cell surface and intracellular signaling. Insertion of ED-B appears to stabilize overall head-to-tail dimerization of two separate Fn chains, which, together with alternating homodimer formation via disulfide bridges at the C-terminal Fn tail, should lead to the known macromolecular fibril formation.


    Organizational Affiliation

    Munich Center for Integrated Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, 85350 Freising-Weihenstephan, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
four-domain fibronectin fragment
A
375Homo sapiensMutation(s): 0 
Gene Names: FN1 (FN)
Find proteins for P02751 (Homo sapiens)
Go to Gene View: FN1
Go to UniProtKB:  P02751
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 211.980α = 90.00
b = 29.115β = 111.42
c = 82.241γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-05-23
    Type: Database references
  • Version 1.2: 2013-06-26
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description