1D66

DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX

• PDB DOI:  https://doi.org/10.2210/pdb1D66/pdb
• NAKB: 1D66

• Classification: TRANSCRIPTION/DNA
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1992-03-06 Released: 1992-03-06 
• Deposition Author(s): Marmorstein, R., Carey, M., Ptashne, M., Harrison, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Work: 0.230 
• R-Value Observed: 0.230 

Literature

DNA recognition by GAL4: structure of a protein-DNA complex.

Marmorstein, R., Carey, M., Ptashne, M., Harrison, S.C.

(1992) Nature 356: 408-414

• PubMed: 1557122 
• DOI: https://doi.org/10.1038/356408a0
• Primary Citation of Related Structures:  
  1D66


• PubMed Abstract: 
  

  A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a dimer to a symmetrical 17-base-pair sequence. A small, Zn(2+)-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.

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Organizational Affiliation: 

Harvard University, Department of Biochemistry and Molecular Biology, Cambridge, Massachusetts.

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: 27.74 kDa 
• Atom Count: 1,762 
• Modelled Residue Count: 152 
• Deposited Residue Count: 170 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (GAL4)	C [auth A], D [auth B]	66	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P04386 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04386  Go to UniProtKB:  P04386

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*GP*AP*GP*GP*AP*CP*AP*GP*TP*CP*CP*TP*CP*C P*GP*G)-3')	A [auth D]	19	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*GP*AP*GP*GP*AP*CP*TP*GP*TP*CP*CP*TP*CP*C P*GP*G)-3')	B [auth E]	19	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	E [auth A], F [auth A], G [auth B], H [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Work: 0.230 
• R-Value Observed: 0.230 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.85	α = 90
b = 80.85	β = 90
c = 73.7	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
TNT	refinement
CORELS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1992-03-06 
Deposition Author(s): Marmorstein, R., Carey, M., Ptashne, M., Harrison, S.C.

Revision History  

• Version 1.0: 1992-03-06
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance