2O4A

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


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 

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This is version 1.1 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan. yamasaki@aist.go.jp



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-binding protein SATB1C [auth A]93Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01826
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*DGP*DCP*DTP*DAP*DAP*DTP*DAP*DTP*DAP*DTP*DGP*DC)-3')A [auth B]12N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*DGP*DCP*DAP*DTP*DAP*DTP*DAP*DTP*DTP*DAP*DGP*DC)-3')B [auth C]12N/A
Protein Feature View
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  • Reference Sequence
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 = 32.659α = 71.34
b = 38.318β = 82.5
c = 40.709γ = 66.63
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALAdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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