4QUF

crystal structure of chromodomain of Rhino with H3K9me3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing.

Le Thomas, A.Stuwe, E.Li, S.Du, J.Marinov, G.Rozhkov, N.Chen, Y.C.Luo, Y.Sachidanandam, R.Toth, K.F.Patel, D.Aravin, A.A.

(2014) Genes Dev 28: 1667-1680

  • DOI: 10.1101/gad.245514.114
  • Primary Citation of Related Structures:  
    4QUC, 4QUF

  • PubMed Abstract: 
  • Small noncoding RNAs that associate with Piwi proteins, called piRNAs, serve as guides for repression of diverse transposable elements in germ cells of metazoa. In Drosophila, the genomic regions that give rise to piRNAs, the so-called piRNA clusters, are transcribed to generate long precursor molecules that are processed into mature piRNAs ...

    Small noncoding RNAs that associate with Piwi proteins, called piRNAs, serve as guides for repression of diverse transposable elements in germ cells of metazoa. In Drosophila, the genomic regions that give rise to piRNAs, the so-called piRNA clusters, are transcribed to generate long precursor molecules that are processed into mature piRNAs. How genomic regions that give rise to piRNA precursor transcripts are differentiated from the rest of the genome and how these transcripts are specifically channeled into the piRNA biogenesis pathway are not known. We found that transgenerationally inherited piRNAs provide the critical trigger for piRNA production from homologous genomic regions in the next generation by two different mechanisms. First, inherited piRNAs enhance processing of homologous transcripts into mature piRNAs by initiating the ping-pong cycle in the cytoplasm. Second, inherited piRNAs induce installment of the histone 3 Lys9 trimethylation (H3K9me3) mark on genomic piRNA cluster sequences. The heterochromatin protein 1 (HP1) homolog Rhino binds to the H3K9me3 mark through its chromodomain and is enriched over piRNA clusters. Rhino recruits the piRNA biogenesis factor Cutoff to piRNA clusters and is required for efficient transcription of piRNA precursors. We propose that transgenerationally inherited piRNAs act as an epigenetic memory for identification of substrates for piRNA biogenesis on two levels: by inducing a permissive chromatin environment for piRNA precursor synthesis and by enhancing processing of these precursors.


    Organizational Affiliation

    Division of Biology, California Institute of Technology, Pasadena, California 91125, USA;



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RE36324pA, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]68Drosophila melanogasterMutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q7JXA8 (Drosophila melanogaster)
Explore Q7JXA8 
Go to UniProtKB:  Q7JXA8
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
H3(1-15)K9me3 peptideB [auth P], D [auth Q], F [auth R], H [auth T], L [auth U], J [auth V]15N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
B [auth P], D [auth Q], F [auth R], H [auth T], J [auth V], L [auth U]L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.317α = 90
b = 79.932β = 96.41
c = 81.181γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2014-07-10 
  • Released Date: 2014-08-20 
  • Deposition Author(s): Li, S., Patel, D.J.

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-20
    Type: Initial release