5CQQ

Crystal structure of the Drosophila Zeste DNA binding domain in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of Zeste-DNA Complex Reveals a New Modality of DNA Recognition by Homeodomain-Like Proteins

Gao, G.N.Wang, M.Yang, N.Huang, Y.Xu, R.M.

(2015) J Mol Biol 427: 3824-3833

  • DOI: https://doi.org/10.1016/j.jmb.2015.10.008
  • Primary Citation of Related Structures:  
    5CQQ

  • PubMed Abstract: 

    Drosophila Zeste is a DNA binding protein important for chromatin-targeted regulation of gene expression. It is best studied in the context of transvection-a mechanism of interallelic gene regulation involving paired chromosomes-and repression of the expression of white by Zeste mutants. Both of these functions depend on the DNA binding and self-association properties of Zeste, but the underlying structural basis remains unknown. Here we report the crystal structure of the DNA binding domain of Zeste in complex with a 19-bp DNA duplex containing the consensus recognition sequence motif. The structure reveals a helix-turn-helix Myb/homeodomain-like fold with the Zeste-specific insertion sequence forming a short helix and a long loop. Direct base contacts by the major groove binding helix principally account for the sequence-specific recognition, and backbone contacts via the Zeste-specific insertion are mainly responsible for the length requirement and the orientation of DNA. Our structural and biochemical characterizations of the DNA binding property of Zeste uncover an altered DNA binding modality of homeodomain-like proteins, and the structural information should facilitate the unraveling of the intricate mechanism of Zeste in regulation of gene expression.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Regulatory protein zeste
A, B
82Drosophila melanogasterMutation(s): 0 
Gene Names: zCG7803
UniProt
Find proteins for P09956 (Drosophila melanogaster)
Explore P09956 
Go to UniProtKB:  P09956
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09956
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*TP*GP*TP*TP*TP*TP*CP*CP*AP*CP*TP*CP*GP*TP*TP*TP*TP*T)-3')
C, E
19Drosophila melanogaster
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*AP*AP*AP*AP*CP*GP*AP*GP*TP*GP*GP*AP*AP*AP*AP*CP*AP*G)-3')
D, F
19Drosophila melanogaster
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.007α = 90
b = 59.705β = 90
c = 202.16γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31430018
National Natural Science Foundation of ChinaChina31210103914
National Natural Science Foundation of ChinaChina31470719
MOSTChina2015CB856202
CASChinaXDB08010100
CASChinaKJZDEW-L05

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2015-12-09
    Changes: Database references
  • Version 1.2: 2017-10-18
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Refinement description