Fibronectin fragment

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

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This is version 1.2 of the entry. See complete history


Zinc Induces Structural Reorganization of Gelatin Binding Domain from Human Fibronectin and Affects Collagen Binding

Graille, M.Pagano, M.Rose, T.Reboud Ravaux, M.van Tilbeurgh, H.

(2010) Structure 18: 710-718

  • DOI: https://doi.org/10.1016/j.str.2010.03.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Fibronectin is a modular extracellular matrix protein involved in cell adhesion, cell motility, wound healing, and maintenance of cell morphology. It is composed of multiple repeats of three distinct modules: F(I), F(II), and F(III). Various combinations of these modules create fragments able to interact with different constituents of the extracellular matrix. Here, we present the 2.5-A resolution crystal structure of its 45-kDa gelatin-binding domain (GBD; 6F(I)-1F(II)-2F(II)-7F(I)-8F(I)-9F(I)), which also corresponds to the C-terminal half of the migration stimulating factor, a Fn splice variant expressed in human breast cancers. GBD forms a very compact zinc-mediated homodimer, in stark contrast with previous structures of fibronectin fragments. Most remarkably, 8F(I) no longer adopts the canonical F(I) fold but is composed of two long strands that associate with 7F(I) and 9F(I) into a large beta-sheet superdomain. Binding studies in solution confirmed that Zn induces conformational rearrangements and causes loss of binding of Fn-GBD to high-affinity collagen peptides. These data suggest the Zn may play a regulatory role for the cellular functions of fibronectin.

  • Organizational Affiliation

    IBBMC, Université Paris 11, IFR115, CNRS UMR8619, Orsay Cedex F-91405, France. marc.graille@u-psud.fr

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FN1 protein308Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02751 (Homo sapiens)
Explore P02751 
Go to UniProtKB:  P02751
GTEx:  ENSG00000115414 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02751
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 12P

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A]
C24 H50 O13
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
C8 H15 N O6
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.789α = 90
b = 124.789β = 90
c = 60.649γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary