2DGC | pdb_00002dgc

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

• PDB DOI: https://doi.org/10.2210/pdb2DGC/pdb
• NAKB: 2DGC

• Classification: TRANSCRIPTION/DNA
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 1995-09-28 Released: 1996-03-08 
• Deposition Author(s): Keller, W., Koenig, P., Richmond, T.J.

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Experimental Data Snapshot

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

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 Biology 254: 657-667

• PubMed: 7500340 
• 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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.2 kDa 
• Atom Count: 859 
• Modelled Residue Count: 68 
• Deposited Residue Count: 82 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (GCN4)	B [auth A]	63	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P03069  Go to UniProtKB:  P03069

Entity ID: 1
Molecule	Chains	Length	Organism	Image
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]	19	N/A

Experimental Data & Validation

Experimental Data

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

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.66	α = 90
b = 58.66	β = 90
c = 86.88	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
OSCREF	data reduction
OSCKRUNCH	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-03-08 
Deposition Author(s): Keller, W., Koenig, P., Richmond, T.J.

Revision History  

• 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
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references