Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.98 kDa 
• Atom Count: 881 
• Modelled Residue Count: 76 
• Deposited Residue Count: 76 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1YUI

SOLUTION NMR STRUCTURE OF THE GAGA FACTOR/DNA COMPLEX, REGULARIZED MEAN STRUCTURE

• PDB DOI: 10.2210/pdb1YUI/pdb
• NDB: 1YUI

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Drosophila melanogaster
• Mutation(s): No 


• Deposited: 1996-12-31 Released: 1997-12-31 
• Deposition Author(s): Clore, G.M., Omichinski, J.G., Gronenborn, A.M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 1 
• Selection Criteria: REGULARIZED MEAN STRUCTURE 

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

• PubMed: 9033593 
• 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 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.

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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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GAGA-FACTOR	C [auth A]	54	Drosophila melanogaster	Mutation(s): 0  Gene Names: Trl, Adf-2, GAGA, Nc70F, TFGAGA, CG33261
UniProt
Find proteins for Q08605 (Drosophila melanogaster) Explore Q08605  Go to UniProtKB:  Q08605

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*CP*GP*AP*GP*AP*GP*TP*AP*C)-3')	A [auth B]	11	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*AP*CP*TP*CP*TP*CP*GP*GP*C)-3')	B [auth C]	11	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 1 
• Selection Criteria: REGULARIZED MEAN STRUCTURE 
• OLDERADO: 1YUI Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-12-31 
• Released Date: 1997-12-31 
Deposition Author(s): Clore, G.M., Omichinski, J.G., Gronenborn, A.M.

Revision History  

• 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