Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.51 kDa 
• Atom Count: 1658 
• Modelled Residue Count: 190 
• Deposited Residue Count: 234 
• Unique protein chains: 1

1YGS

CRYSTAL STRUCTURE OF THE SMAD4 TUMOR SUPPRESSOR C-TERMINAL DOMAIN

• PDB DOI: 10.2210/pdb1YGS/pdb

• Classification: TUMOUR SUPPRESSOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-10-03 Released: 1998-07-08 
• Deposition Author(s): Shi, Y., Hata, A., Lo, R.S., Massague, J., Pavletich, N.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.279 
• R-Value Work: 0.219 
• R-Value Observed: 0.219 

Literature

A structural basis for mutational inactivation of the tumour suppressor Smad4.

Shi, Y., Hata, A., Lo, R.S., Massague, J., Pavletich, N.P.

(1997) Nature 388: 87-93

• PubMed: 9214508 
• DOI: 10.1038/40431
• Primary Citation of Related Structures:  
  1YGS


• PubMed Abstract: 
  

The Smad4/DPC4 tumour suppressor is inactivated in nearly half of pancreatic carcinomas and to a lesser extent in a variety of other cancers. Smad4/DPC4, and the related tumour suppressor Smad2, belong to the SMAD family of proteins that mediate signalling by the TGF-beta/activin/BMP-2/4 cytokine superfamily from receptor Ser/Thr protein kinases at the cell surface to the nucleus. SMAD proteins, which are phosphorylated by the activated receptor, propagate the signal, in part, through homo- and hetero-oligomeric interactions. Smad4/DPC4 plays a central role as it is the shared hetero-oligomerization partner of the other SMADs. The conserved carboxy-terminal domains of SMADs are sufficient for inducing most of the ligand-specific effects, and are the primary targets of tumorigenic inactivation. We now describe the crystal structure of the C-terminal domain (CTD) of the Smad4/DPC4 tumour suppressor, determined at 2.5 A resolution. The structure reveals that the Smad4/DPC4 CTD forms a crystallographic trimer through a conserved protein-protein interface, to which the majority of the tumour-derived missense mutations map. These mutations disrupt homo-oligomerization in vitro and in vivo, indicating that the trimeric assembly of the Smad4/DPC4 CTD is critical for signalling and is disrupted by tumorigenic mutations.

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Organizational Affiliation: 

Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York 10021, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SMAD4	A	234	Homo sapiens	Mutation(s): 0  Gene Names: SMAD4, DPC4, MADH4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13485 (Homo sapiens) Explore Q13485  Go to UniProtKB:  Q13485
PHAROS:  Q13485 GTEx:  ENSG00000141646

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.279 
• R-Value Work: 0.219 
• R-Value Observed: 0.219 
• Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 197.842	α = 90
b = 197.842	β = 90
c = 197.842	γ = 90

Software Package:

Software Name	Purpose
DM	model building
SQUASH	phasing
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-10-03 
• Released Date: 1998-07-08 
Deposition Author(s): Shi, Y., Hata, A., Lo, R.S., Massague, J., Pavletich, N.P.

Revision History  

• Version 1.0: 1998-07-08
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance