4GAT

SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13BP DNA CONTAINING A CGATA SITE, REGULARIZED MEAN STRUCTURE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 35 
  • Conformers Submitted: 
  • Selection Criteria: REGULARIZED MEAN STRUCTURE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The solution structure of a fungal AREA protein-DNA complex: an alternative binding mode for the basic carboxyl tail of GATA factors.

Starich, M.R.Wikstrom, M.Arst Jr., H.N.Clore, G.M.Gronenborn, A.M.

(1998) J Mol Biol 277: 605-620

  • DOI: 10.1006/jmbi.1998.1625
  • Primary Citation of Related Structures:  
    4GAT, 5GAT

  • PubMed Abstract: 
  • The solution structure of a complex between the DNA binding domain of a fungal GATA factor and a 13 base-pair oligonucleotide containing its physiologically relevant CGATAG target sequence has been determined by multidimensional nuclear magnetic resonance spectroscopy ...

    The solution structure of a complex between the DNA binding domain of a fungal GATA factor and a 13 base-pair oligonucleotide containing its physiologically relevant CGATAG target sequence has been determined by multidimensional nuclear magnetic resonance spectroscopy. The AREA DNA binding domain, from Aspergillus nidulans, possesses a single Cys2-Cys2 zinc finger module and a basic C-terminal tail, which recognize the CGATAG element via an extensive network of hydrophobic interactions with the bases in the major groove and numerous non-specific contacts along the sugar-phosphate backbone. The zinc finger core of the AREA DNA binding domain has the same global fold as that of the C-terminal DNA binding domain of chicken GATA-1. In contrast to the complex with the DNA binding domain of GATA-1 in which the basic C-terminal tail wraps around the DNA and lies in the minor groove, the structure of complex with the AREA DNA binding domain reveals that the C-terminal tail of the fungal domain runs parallel with the sugar phosphate backbone along the edge of the minor groove. This difference is principally attributed to amino acid substitutions at two positions of the AREA DNA binding domain (Val55, Asn62) relative to that of GATA-1 (Gly55, Lys62). The impact of the different C-terminal tail binding modes on the affinity and specificity of GATA factors is discussed.


    Organizational Affiliation

    National Institute of Diabetes and Digestive Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NITROGEN REGULATORY PROTEIN AREAC [auth A]66Aspergillus nidulansMutation(s): 0 
Gene Names: POTENTIAL
UniProt
Find proteins for P17429 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Explore P17429 
Go to UniProtKB:  P17429
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17429
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*AP*GP*CP*GP*AP*TP*AP*GP*AP*GP*AP*C)-3')A [auth B]13N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*CP*GP*CP*TP*G)-3')B [auth C]13N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 35 
  • Conformers Submitted: 
  • Selection Criteria: REGULARIZED MEAN STRUCTURE 
  • OLDERADO: 4GAT Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-16
    Changes: Database references, Derived calculations, Other