1MR1 | pdb_00001mr1

Crystal Structure of a Smad4-Ski Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.280 (Depositor) 
  • R-Value Work: 
    0.231 (Depositor) 
  • R-Value Observed: 
    0.235 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1MR1

This is version 1.3 of the entry. See complete history

Literature

Structural Mechanism of Smad4 Recognition by the Nuclear Oncoprotein Ski: Insights on Ski-mediated Repression of TGF-beta Signaling

Wu, J.-W.Krawitz, A.R.Chai, J.Li, W.Zhang, F.Luo, K.Shi, Y.

(2002) Cell 111: 357-367

  • DOI: https://doi.org/10.1016/s0092-8674(02)01006-1
  • Primary Citation Related Structures: 
    1MR1

  • PubMed Abstract: 

    The Ski family of nuclear oncoproteins represses TGF-beta signaling through interactions with the Smad proteins. The crystal structure of the Smad4 binding domain of human c-Ski in complex with the MH2 domain of Smad4 reveals specific recognition of the Smad4 L3 loop region by a highly conserved interaction loop (I loop) from Ski. The Ski binding surface on Smad4 significantly overlaps with that required for binding of the R-Smads. Indeed, Ski disrupts the formation of a functional complex between the Co- and R-Smads, explaining how it could lead to repression of TGF-beta, activin, and BMP responses. Intriguingly, the structure of the Ski fragment, stabilized by a bound zinc atom, resembles the SAND domain, in which the corresponding I loop is responsible for DNA binding.


  • Organizational Affiliation
    • Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544, USA.

Macromolecule Content 

  • Total Structure Weight: 74.45 kDa 
  • Atom Count: 4,684 
  • Modeled Residue Count: 581 
  • Deposited Residue Count: 668 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mothers against decapentaplegic homolog 4
A, B
235Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13485 (Homo sapiens)
Explore Q13485 
Go to UniProtKB:  Q13485
PHAROS:  Q13485
GTEx:  ENSG00000141646 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13485
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ski oncogene
C, D
99Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P12755 (Homo sapiens)
Explore P12755 
Go to UniProtKB:  P12755
PHAROS:  P12755
GTEx:  ENSG00000157933 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12755
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.280 (Depositor) 
  • R-Value Work:  0.231 (Depositor) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.8α = 90
b = 109.8β = 90
c = 141.1γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-21
    Type: Initial release
  • Version 1.1: 2008-05-05
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations