3TUO | pdb_00003tuo

Crystal structure of N-terminal domain of DNA-binding protein satb1

• PDB DOI: https://doi.org/10.2210/pdb3TUO/pdb

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


• Deposited: 2011-09-17 Released: 2012-02-01 
• Deposition Author(s): Wang, Z., Yang, X., Long, J., Shen, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.218 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Literature

The structural basis for the oligomerization of the N-terminal domain of SATB1

Wang, Z., Yang, X., Chu, X., Zhang, J., Zhou, H., Shen, Y., Long, J.

(2012) Nucleic Acids Res 40: 4193-4202

• PubMed: 22241778 
• DOI: https://doi.org/10.1093/nar/gkr1284
• Primary Citation Related Structures: 
  3TUO


• PubMed Abstract: 
  

  Special AT-rich sequence-binding protein 1 (SATB1) is a global chromatin organizer and gene expression regulator essential for T-cell development and breast cancer tumor growth and metastasis. The oligomerization of the N-terminal domain of SATB1 is critical for its biological function. We determined the crystal structure of the N-terminal domain of SATB1. Surprisingly, this domain resembles a ubiquitin domain instead of the previously proposed PDZ domain. Our results also reveal that SATB1 can form a tetramer through its N-terminal domain. The tetramerization of SATB1 plays an essential role in its binding to highly specialized DNA sequences. Furthermore, isothermal titration calorimetry results indicate that the SATB1 tetramer can bind simultaneously to two DNA targets. Based on these results, we propose a molecular model whereby SATB1 regulates the expression of multiple genes both locally and at a distance.

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Organizational Affiliation: 
• State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 46.63 kDa 
• Atom Count: 3,277 
• Modeled Residue Count: 391 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein SATB1	A, B, C, D	105	Homo sapiens	Mutation(s): 0  Gene Names: SATB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q01826 (Homo sapiens) Explore Q01826  Go to UniProtKB:  Q01826
PHAROS:  Q01826 GTEx:  ENSG00000182568

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.218 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.895	α = 90
b = 71.027	β = 90
c = 153.763	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-01 
Deposition Author(s): Wang, Z., Yang, X., Long, J., Shen, Y.

Revision History  

• Version 1.0: 2012-02-01
  Type: Initial release
  
• Version 1.1: 2013-06-26
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references