Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.39 kDa 
• Atom Count: 1290 
• Residue Count: 107 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1ZAA

ZINC FINGER-DNA RECOGNITION: CRYSTAL STRUCTURE OF A ZIF268-DNA COMPLEX AT 2.1 ANGSTROMS

• DOI: 10.2210/pdb1ZAA/pdb
• NDB: PDT006

• Classification: TRANSCRIPTION/DNA
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 1992-09-17 Released: 1993-10-31 
• Deposition Author(s): Pavletich, N.P., Pabo, C.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Work: 0.182 
• R-Value Observed: 0.182 

Literature

Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A.

Pavletich, N.P., Pabo, C.O.

(1991) Science 252: 809-817

• PubMed: 2028256 
• DOI: 10.1126/science.2028256
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The zinc finger DNA-binding motif occurs in many proteins that regulate eukaryotic gene expression. The crystal structure of a complex containing the three zinc fingers from Zif268 (a mouse immediate early protein) and a consensus DNA-binding site has been determined at 2.1 angstroms resolution and refined to a crystallographic R factor of 18.2 percent. In this complex, the zinc fingers bind in the major groove of B-DNA and wrap part way around the double helix. Each finger has a similar relation to the DNA and makes its primary contacts in a three-base pair subsite. Residues from the amino-terminal portion of an alpha helix contact the bases, and most of the contracts are made with the guanine-rich strand of the DNA. This structure provides a framework for understanding how zinc fingers recognize DNA and suggests that this motif may provide a useful basis for the design of novel DNA-binding proteins.

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Organizational Affiliation: 

Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (ZIF268)	C	87	Mus musculus	Mutation(s): 0  Gene Names: Egr1, Egr-1, Krox-24
Find proteins for P08046 (Mus musculus) Go to UniProtKB:  P08046
NIH Common Fund Data Resources
IMPC  MGI:95295

Entity ID: 1
Molecule	Chains	Length	Organism
DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*GP*T)-3')	A	11	N/A

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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Work: 0.182 
• R-Value Observed: 0.182 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.4	α = 90
b = 56.2	β = 90
c = 130.8	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1992-09-17 
• Released Date: 1993-10-31 
Deposition Author(s): Pavletich, N.P., Pabo, C.O.

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