1A1L

ZIF268 ZINC FINGER-DNA COMPLEX (GCAC SITE)


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 

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This is version 1.4 of the entry. See complete history


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

  • 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. Here we report the X-ray crystal structures of zinc finger-DNA complexes involving three variants of Zif268, with multiple changes in the recognition helix of finger one. We describe the structure of each of these three-finger peptides bound to its corresponding target site. To help elucidate the differential basis for site-specific recognition, the structures of four other complexes containing various combinations of these peptides with alternative binding sites have also been determined. The protein-DNA contacts observed in these complexes reveal the basis for the specificity demonstrated by these Zif268 variants. Many, but not all, of the contacts can be rationalized in terms of a recognition code, but the predictive value of such a code is limited. The structures illustrate how modest changes in the docking arrangement accommodate the new sidechain-base and sidechain-phosphate interactions. Such adaptations help explain the versatility of naturally occurring zinc finger proteins and their utility in design.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (ZIF268 ZINC FINGER PEPTIDE)C [auth A]90Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P08046 (Mus musculus)
Explore P08046 
Go to UniProtKB:  P08046
IMPC:  MGI:95295
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08046
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*AP*C)-3')A [auth B]11N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*GP*TP*GP*CP*CP*CP*AP*CP*GP*C)-3')B [auth C]11N/A
Sequence Annotations
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  • Reference Sequence
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 = 43.3α = 90
b = 55.9β = 90
c = 132.5γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2024-05-22
    Changes: Data collection