1YUJ

SOLUTION NMR STRUCTURE OF THE GAGA FACTOR/DNA COMPLEX, 50 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 50 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The solution structure of a specific GAGA factor-DNA complex reveals a modular binding mode.

Omichinski, J.G.Pedone, P.V.Felsenfeld, G.Gronenborn, A.M.Clore, G.M.

(1997) Nat Struct Biol 4: 122-132

  • DOI: 10.1038/nsb0297-122
  • Primary Citation of Related Structures:  
    1YUI, 1YUJ

  • PubMed Abstract: 
  • The structure of a complex between the DNA binding domain of the GAGA factor (GAGA-DBD) and an oligonucleotide containing its GAGAG consensus binding site has been determined by nuclear magnetic resonance spectroscopy. The GAGA-DBD comprises a single classical Cys2-His2 zinc finger core, and an N-terminal extension containing two highly basic regions, BR1 and BR2 ...

    The structure of a complex between the DNA binding domain of the GAGA factor (GAGA-DBD) and an oligonucleotide containing its GAGAG consensus binding site has been determined by nuclear magnetic resonance spectroscopy. The GAGA-DBD comprises a single classical Cys2-His2 zinc finger core, and an N-terminal extension containing two highly basic regions, BR1 and BR2. The zinc finger core binds in the major groove and recognizes the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. Unlike the latter, which require tandem zinc finger repeats with a minimum of two units for high affinity binding, the GAGA-DBD makes use of only a single finger complemented by BR1 and BR2. BR2 forms a helix that interacts in the major groove recognizing the last G of the consensus, while BR1 wraps around the DNA in the minor groove and recognizes the A in the fourth position of the consensus. The implications of the structure of the GAGA-DBD-DNA complex for chromatin remodelling are discussed.


    Organizational Affiliation

    Laboratories of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
GAGA-FACTORC [auth A]54Drosophila melanogasterMutation(s): 0 
Gene Names: TrlAdf-2GAGANc70FTFGAGACG33261
UniProt
Find proteins for Q08605 (Drosophila melanogaster)
Explore Q08605 
Go to UniProtKB:  Q08605
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08605
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*CP*CP*GP*AP*GP*AP*GP*TP*AP*C)-3')A [auth B]11N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*TP*AP*CP*TP*CP*TP*CP*GP*GP*C)-3')B [auth C]11N/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 Submitted: 50 
  • OLDERADO: 1YUJ Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-12-31
    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: 2022-03-02
    Changes: Database references, Derived calculations, Other