7VRF

Crystal structure of Oxpecker chromodomain in complex with H3K9me3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the chromodomain of Oxpecker in complex with histone H3 lysine 9 trimethylation reveal a transposon silencing mechanism by heterodimerization.

Jin, Z.Yu, B.Huang, Y.

(2023) Biochem Biophys Res Commun 652: 95-102

  • DOI: https://doi.org/10.1016/j.bbrc.2023.02.045
  • Primary Citation of Related Structures:  
    7VRF

  • PubMed Abstract: 

    Oxpecker, the homolog of Rhino/HP1D, exclusively expressed in Drosophila ovaries, belongs to the Heterochromatin Protein 1 family, as does Rhino. Rhi recognizes piRNA clusters enriched with the heterochromatin marker H3K9me3 via its N-terminal chromodomain and recruits Deadlock via its C-terminal chromoshadow domain, further recruits Moonshiner, a paralog of the TATA box-binding protein-related factor 2 large subunits, to promote transcription of piRNA precursors, thereby protecting the genome. Despite Oxp possessing only the chromodomain, its loss leads to the upregulation of transposons in the female germline. In this study, we solved the crystal structure of the Oxp chromodomain in complex with the histone H3K9me3 peptide. As the Oxp chromodomain dimerizes, two H3K9me3 peptides bind to the Oxp chromodomain in an antiparallel manner. ITC experiments and site-directed mutagenesis experiments showed that E44 determines Oxp's five-fold stronger binding ability to H3K9me3 than that of Rhi. In addition, we found that Oxp and Rhi can form a heterodimer, which may shed light on the molecular mechanism by which Oxp regulates transposon silencing in the absence of CSD.


  • Organizational Affiliation

    Department of General Surgery, Shanghai Key Laboratory of Biliary Tract Disease Research, State Key Laboratory of Oncogenes and Related Genes, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, 200092, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxpecker
A, B
71Drosophila melanogasterMutation(s): 0 
Gene Names: OxpDmel\CG18186OXPCG18186Dmel_CG18186
UniProt
Find proteins for A1ZAW9 (Drosophila melanogaster)
Explore A1ZAW9 
Go to UniProtKB:  A1ZAW9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1ZAW9
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
H3K9me3
C, D
11Drosophila melanogasterMutation(s): 0 
UniProt
Find proteins for P02299 (Drosophila melanogaster)
Explore P02299 
Go to UniProtKB:  P02299
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02299
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
C, D
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.197 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.421α = 61.228
b = 37.455β = 88.787
c = 38.757γ = 74.943
Software Package:
Software NamePurpose
HKL-3000data collection
PHENIXrefinement
Cootmodel building
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171186

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-26
    Type: Initial release
  • Version 1.1: 2023-05-17
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description