2DGC

GCN4 BASIC DOMAIN, LEUCINE ZIPPER COMPLEXED WITH ATF/CREB SITE DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of a bZIP/DNA complex at 2.2 A: determinants of DNA specific recognition.

Keller, W., Konig, P., Richmond, T.J.

(1995) J Mol Biol 254: 657-667

  • DOI: https://doi.org/10.1006/jmbi.1995.0645
  • Primary Citation of Related Structures:  
    2DGC

  • PubMed Abstract: 

    • The X-ray structure of the GCN4-bZIP protein bound to DNA containing the ATF/CREB recognition sequence has been refined at 2.2 A. The water-mediated interactions between the basic domain and DNA are revealed, and combined with a more accurate description of the direct contacts, further clarify how binding specificity is achieved ...

    The X-ray structure of the GCN4-bZIP protein bound to DNA containing the ATF/CREB recognition sequence has been refined at 2.2 A. The water-mediated interactions between the basic domain and DNA are revealed, and combined with a more accurate description of the direct contacts, further clarify how binding specificity is achieved. Water molecules extend the interactions of both invariant basic domain residues, asparagine 235 and arginine 243, beyond their direct base contacts. The slight bending of the basic domain alpha-helix around the DNA facilitates the linking of arginine 241, 243 and 245 to main-chain carbonyl oxygen atoms via water molecules, apparently stabilizing interactions with the DNA.

    Related Citations: 
    • The X-Ray Structure of the GCN4-bZIP Bound to ATF/CREB Site DNA Shows the Complex Depends on DNA Flexibility
      Koenig, P., Richmond, T.J.
      (1993) J Mol Biol 233: 139
    • The GCN4 Basic Region Leucine Zipper Binds DNA as a Dimer of Uninterrupted Alpha Helices: Crystal Structure of the Protein-DNA Complex
      Ellenberger, T.E., Brandl, C.J., Struhl, K., Harrison, S.C.
      (1992) Cell 71: 1223
    Organizational Affiliation: 

    Institut für Molekularbiologie und Biophysik, ETH-Hönggerberg, Zurich, Switzerland.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (GCN4)B [auth A]63Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P03069 
Go to UniProtKB:  P03069
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03069
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*GP*GP*AP*GP*AP*TP*GP*AP*CP*GP*TP*CP*AP*TP*CP*T P*CP*C)-3')A [auth B]19N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.66α = 90
b = 58.66β = 90
c = 86.88γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
OSCREFdata reduction
OSCKRUNCHdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance