1A1L

ZIF268 ZINC FINGER-DNA COMPLEX (GCAC SITE)

• PDB DOI:  https://doi.org/10.2210/pdb1A1L/pdb
• NAKB: 1A1L

• Classification: TRANSCRIPTION/DNA
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1997-12-10 Released: 1998-06-17 
• Deposition Author(s): Elrod-Erickson, M., Benson, T.E., Pabo, C.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.267 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

Literature

High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition.

Elrod-Erickson, M., Benson, T.E., Pabo, C.O.

(1998) Structure 6: 451-464

• PubMed: 9562555 
• DOI: https://doi.org/10.1016/s0969-2126(98)00047-1
• Primary Citation of Related Structures:  
  1A1F, 1A1G, 1A1H, 1A1I, 1A1J, 1A1K, 1A1L


• PubMed Abstract: 
  

Zinc fingers of the Cys2-His2 class comprise one of the largest families of eukaryotic DNA-binding motifs and recognize a diverse set of DNA sequences. These proteins have a relatively simple modular structure and key base contacts are typically made by a few residues from each finger. These features make the zinc finger motif an attractive system for designing novel DNA-binding proteins and for exploring fundamental principles of protein-DNA recognition.

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Related Citations: 

• Zif268 Protein-DNA Complex Refined at 1.6 A: A Model System for Understanding Zinc Finger-DNA Interactions
  Elrod-Erickson, M., Rould, M.A., Nekludova, L., Pabo, C.O.
  (1996) Structure 4: 1171

• Zinc Finger Phage: Affinity Selection of Fingers with New DNA-Binding Specificities
  Rebar, E.J., Pabo, C.O.
  (1994) Science 263: 671

• 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

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Organizational Affiliation: 

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.76 kDa 
• Atom Count: 1,268 
• Modelled Residue Count: 107 
• Deposited Residue Count: 112 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (ZIF268 ZINC FINGER PEPTIDE)	C [auth A]	90	Mus musculus	Mutation(s): 0  Gene Names: Egr1, Egr-1, Krox-24
UniProt & NIH Common Fund Data Resources
Find proteins for P08046 (Mus musculus) Explore P08046  Go to UniProtKB:  P08046
IMPC:  MGI:95295

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*AP*C)-3')	A [auth B]	11	N/A

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.267 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.3	α = 90
b = 55.9	β = 90
c = 132.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-06-17 
Deposition Author(s): Elrod-Erickson, M., Benson, T.E., Pabo, C.O.

Revision History  

• Version 1.0: 1998-06-17
  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: 2023-08-02
  Changes: Database references, Derived calculations, Refinement description