1SBX | pdb_00001sbx

Crystal structure of the Dachshund-homology domain of human SKI

• PDB DOI: https://doi.org/10.2210/pdb1SBX/pdb

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-02-11 Released: 2004-05-25 
• Deposition Author(s): Wilson, J.J., Malakhova, M., Zhang, R., Joachimiak, A., Hegde, R.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.206 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Crystal Structure of the Dachshund Homology Domain of human SKI

Wilson, J.J., Malakhova, M., Zhang, R., Joachimiak, A., Hegde, R.S.

(2004) Structure 12: 785-792

• PubMed: 15130471 
• DOI: https://doi.org/10.1016/j.str.2004.02.035
• Primary Citation Related Structures: 
  1SBX


• PubMed Abstract: 
  

  The nuclear protooncoprotein SKI negatively regulates transforming growth factor-beta (TGF-beta) signaling in cell growth and differentiation. It directly interacts with the Smads and, by various mechanisms, represses the transcription of TGF-beta-responsive genes. SKI is a multidomain protein that includes a domain bearing high sequence similarity with the retinal determination protein Dachshund (the Dachshund homology domain, DHD). The SKI-DHD has been implicated in SMAD-2/3, N-CoR, SKIP, and PML-RARalpha binding. The 1.65 A crystal structure of the Dachshund homology domain of human SKI is reported here. The SKI-DHD adopts a mixed alpha/beta structure which includes features found in the forkhead/winged-helix family of DNA binding proteins, although SKI-DHD is not a DNA binding domain. Residues that form a contiguous surface patch on SKI-DHD are conserved within the Ski/Sno family and with Dachshund, suggesting that this domain may mediate intermolecular interactions common to these proteins.

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Organizational Affiliation: 
• Division of Developmental Biology, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.87 kDa 
• Atom Count: 944 
• Modeled Residue Count: 106 
• Deposited Residue Count: 106 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ski oncogene	A	106	Homo sapiens	Mutation(s): 3  Gene Names: SKI
UniProt & NIH Common Fund Data Resources
Find proteins for P12755 (Homo sapiens) Explore P12755  Go to UniProtKB:  P12755
PHAROS:  P12755 GTEx:  ENSG00000157933

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.206 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.927	α = 90
b = 46.633	β = 93.97
c = 35.729	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-25 
Deposition Author(s): Wilson, J.J., Malakhova, M., Zhang, R., Joachimiak, A., Hegde, R.S.

Revision History  

• Version 1.0: 2004-05-25
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary