1YSA | pdb_00001ysa

THE GCN4 BASIC REGION LEUCINE ZIPPER BINDS DNA AS A DIMER OF UNINTERRUPTED ALPHA HELICES: CRYSTAL STRUCTURE OF THE PROTEIN-DNA COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1YSA/pdb
• NAKB: 1YSA

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


• Deposited: 1993-08-09 Released: 1993-10-31 
• Deposition Author(s): Ellenberger, T.E., Brandl, C.J., Struhl, K., Harrison, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Observed: 
  0.230 (Depositor) 

Literature

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: 1223-1237

• PubMed: 1473154 
• DOI: https://doi.org/10.1016/s0092-8674(05)80070-4
• Primary Citation Related Structures: 
  1YSA


• PubMed Abstract: 
  

  The yeast transcriptional activator GCN4 is 1 of over 30 identified eukaryotic proteins containing the basic region leucine zipper (bZIP) DNA-binding motif. We have determined the crystal structure of the GCN4 bZIP element complexed with DNA at 2.9 A resolution. The bZIP dimer is a pair of continuous alpha helices that form a parallel coiled coil over their carboxy-terminal 30 residues and gradually diverge toward their amino termini to pass through the major groove of the DNA-binding site. The coiled-coil dimerization interface is oriented almost perpendicular to the DNA axis, giving the complex the appearance of the letter T. There are no kinks or sharp bends in either bZIP monomer. Numerous contacts to DNA bases and phosphate oxygens are made by basic region residues that are conserved in the bZIP protein family. The details of the bZIP dimer interaction with DNA can explain recognition of the AP-1 site by the GCN4 protein.

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Organizational Affiliation: 
• Harvard University, Department of Biochemistry and Molecular Biology, Cambridge, Massachusetts 02138.

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: 26.05 kDa 
• Atom Count: 1,772 
• Modeled Residue Count: 154 
• Deposited Residue Count: 156 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (GCN4)	C, D	58	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*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*AP*TP*CP*CP*A P*GP*TP*T)-3')	A	20	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*AP*CP*TP*GP*GP*AP*TP*GP*AP*GP*TP*CP*AP*TP*A P*GP*GP*A)-3')	B	20	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.13	α = 90
b = 88.54	β = 90
c = 59.24	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-10-31 
Deposition Author(s): Ellenberger, T.E., Brandl, C.J., Struhl, K., Harrison, S.C.

Revision History  

• Version 1.0: 1993-10-31
  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