1GAT

SOLUTION STRUCTURE OF THE SPECIFIC DNA COMPLEX OF THE ZINC CONTAINING DNA BINDING DOMAIN OF THE ERYTHROID TRANSCRIPTION FACTOR GATA-1 BY MULTIDIMENSIONAL NMR


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1.

Omichinski, J.G.Clore, G.M.Schaad, O.Felsenfeld, G.Trainor, C.Appella, E.Stahl, S.J.Gronenborn, A.M.

(1993) Science 261: 438-446

  • DOI: https://doi.org/10.1126/science.8332909
  • Primary Citation of Related Structures:  
    1GAT, 1GAU

  • PubMed Abstract: 

    The three-dimensional solution structure of a complex between the DNA binding domain of the chicken erythroid transcription factor GATA-1 and its cognate DNA site has been determined with multidimensional heteronuclear magnetic resonance spectroscopy. The DNA binding domain consists of a core which contains a zinc coordinated by four cysteines and a carboxyl-terminal tail. The core is composed of two irregular antiparallel beta sheets and an alpha helix, followed by a long loop that leads into the carboxyl-terminal tail. The amino-terminal part of the core, including the helix, is similar in structure, although not in sequence, to the amino-terminal zinc module of the glucocorticoid receptor DNA binding domain. In the other regions, the structures of these two DNA binding domains are entirely different. The DNA target site in contact with the protein spans eight base pairs. The helix and the loop connecting the two antiparallel beta sheets interact with the major groove of the DNA. The carboxyl-terminal tail, which is an essential determinant of specific binding, wraps around into the minor groove. The complex resembles a hand holding a rope with the palm and fingers representing the protein core and the thumb, the carboxyl-terminal tail. The specific interactions between GATA-1 and DNA in the major groove are mainly hydrophobic in nature, which accounts for the preponderance of thymines in the target site. A large number of interactions are observed with the phosphate backbone.


  • Organizational Affiliation

    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ERYTHROID TRANSCRIPTION FACTOR GATA-1C [auth A]60Gallus gallusMutation(s): 0 
UniProt
Find proteins for P17678 (Gallus gallus)
Explore P17678 
Go to UniProtKB:  P17678
Entity Groups  
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UniProt GroupP17678
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*GP*AP*TP*AP*AP*AP*C)3')A [auth B]8N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*TP*TP*TP*AP*TP*CP*T)-3')B [auth C]8N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-09-05
    Changes: Database references
  • Version 1.4: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Other