1MR1

Crystal Structure of a Smad4-Ski Complex

• PDB DOI:  https://doi.org/10.2210/pdb1MR1/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-09-17 Released: 2003-01-21 
• Deposition Author(s): Wu, J.-W., Krawitz, A.R., Chai, J., Li, W., Zhang, F., Luo, K., Shi, Y.

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Experimental Data Snapshot

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

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

• PubMed: 12419246 
• DOI: https://doi.org/10.1016/s0092-8674(02)01006-1
• Primary Citation of 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mothers against decapentaplegic homolog 4	A, B	235	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ski oncogene	C, D	99	Homo sapiens	Mutation(s): 0  Gene Names: SKI
UniProt & NIH Common Fund Data Resources
Find proteins for P12755 (Homo sapiens) Explore P12755  Go to UniProtKB:  P12755
PHAROS:  P12755

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth C], F [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.280 
• R-Value Work: 0.231 
• R-Value Observed: 0.235 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.8	α = 90
b = 109.8	β = 90
c = 141.1	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-01-21 
Deposition Author(s): Wu, J.-W., Krawitz, A.R., Chai, J., Li, W., Zhang, F., Luo, K., Shi, Y.

Revision History  

• 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