3M7P | pdb_00003m7p

Fibronectin fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.219 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3M7P

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

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 Related Structures: 
    3M7P

  • 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 <marc.graille@u-psud.fr>

Macromolecule Content 

  • Total Structure Weight: 37.33 kDa 
  • Atom Count: 2,530 
  • Modeled Residue Count: 301 
  • Deposited Residue Count: 308 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
PHAROS:  P02751
GTEx:  ENSG00000115414 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02751
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P02751-15
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
12P

Query on 12P



Download:Ideal Coordinates CCD File
L [auth A],
M [auth A]
DODECAETHYLENE GLYCOL
C24 H50 O13
WRZXKWFJEFFURH-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN

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]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.219 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
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
SHARPphasing
BUSTERrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



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
  • Version 1.3: 2024-10-09
    Changes: Data collection, Database references, Structure summary