2O4A

Crystal Structure of the N-terminal CUT Domain of SATB1 Bound to Matrix Attachment Region DNA

• PDB DOI:  https://doi.org/10.2210/pdb2O4A/pdb
• NAKB: 2O4A

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-12-04 Released: 2007-08-14 
• Deposition Author(s): Yamasaki, K., Akiba, T., Harata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.282 
• R-Value Work: 0.245 
• R-Value Observed: 0.245 

Literature

Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1.

Yamasaki, K., Akiba, T., Yamasaki, T., Harata, K.

(2007) Nucleic Acids Res 35: 5073-5084

• PubMed: 17652321 
• DOI: https://doi.org/10.1093/nar/gkm504
• Primary Citation of Related Structures:  
  2O49, 2O4A


• PubMed Abstract: 
  

Special AT-rich sequence binding protein 1 (SATB1) regulates gene expression essential in immune T-cell maturation and switching of fetal globin species, by binding to matrix attachment regions (MARs) of DNA and inducing a local chromatin remodeling. Previously we have revealed a five-helix structure of the N-terminal CUT domain, which is essentially the folded region in the MAR-binding domain, of human SATB1 by NMR. Here we determined crystal structure of the complex of the CUT domain and a MAR DNA, in which the third helix of the CUT domain deeply enters the major groove of DNA in the B-form. Bases of 5'-CTAATA-3' sequence are contacted by this helix, through direct and water-mediated hydrogen bonds and apolar and van der Waals contacts. Mutations at conserved base-contacting residues, Gln402 and Gly403, reduced the DNA-binding activity, which confirmed the importance of the observed interactions involving these residues. A significant number of equivalent contacts are observed also for typically four-helix POU-specific domains of POU-homologous proteins, indicating that these domains share a common framework of the DNA-binding mode, recognizing partially similar DNA sequences.

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Organizational Affiliation: 

Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.28 kDa 
• Atom Count: 1,290 
• Modelled Residue Count: 108 
• Deposited Residue Count: 117 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein SATB1	C [auth A]	93	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

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DGP*DCP*DTP*DAP*DAP*DTP*DAP*DTP*DAP*DTP*DGP*DC)-3')	A [auth B]	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DGP*DCP*DAP*DTP*DAP*DTP*DAP*DTP*DTP*DAP*DGP*DC)-3')	B [auth C]	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.282 
• R-Value Work: 0.245 
• R-Value Observed: 0.245 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.659	α = 71.34
b = 38.318	β = 82.5
c = 40.709	γ = 66.63

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-14 
Deposition Author(s): Yamasaki, K., Akiba, T., Harata, K.

Revision History  

• Version 1.0: 2007-08-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance