5XYW

Crystal structure of drosophila simulans Rhino chromoshadow domain in complex with N-terminal domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into Rhino-Deadlock complex for germline piRNA cluster specification

Yu, B.Lin, Y.A.Parhad, S.S.Jin, Z.Ma, J.Theurkauf, W.E.Zhang, Z.Z.Huang, Y.

(2018) EMBO Rep 19

  • DOI: https://doi.org/10.15252/embr.201745418
  • Primary Citation of Related Structures:  
    5XYV, 5XYW

  • PubMed Abstract: 

    PIWI-interacting RNAs (piRNAs) silence transposons in germ cells to maintain genome stability and animal fertility. Rhino, a rapidly evolving heterochromatin protein 1 (HP1) family protein, binds Deadlock in a species-specific manner and so defines the piRNA-producing loci in the Drosophila genome. Here, we determine the crystal structures of Rhino-Deadlock complex in Drosophila melanogaster and simulans In both species, one Rhino binds the N-terminal helix-hairpin-helix motif of one Deadlock protein through a novel interface formed by the beta-sheet in the Rhino chromoshadow domain. Disrupting the interface leads to infertility and transposon hyperactivation in flies. Our structural and functional experiments indicate that electrostatic repulsion at the interaction interface causes cross-species incompatibility between the sibling species. By determining the molecular architecture of this piRNA-producing machinery, we discover a novel HP1-partner interacting mode that is crucial to piRNA biogenesis and transposon silencing. We thus explain the cross-species incompatibility of two sibling species at the molecular level.


  • Organizational Affiliation

    State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rhino
A, B
68Drosophila simulansMutation(s): 0 
Gene Names: rhiDsim\GD27086Dsimw501_GD27086GD25457
UniProt
Find proteins for Q49BI5 (Drosophila simulans)
Explore Q49BI5 
Go to UniProtKB:  Q49BI5
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UniProt GroupQ49BI5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GD21652
C, D
60Drosophila simulansMutation(s): 0 
Gene Names: Dsim\GD21652Dsim_GD21652GD21652
UniProt
Find proteins for B4Q3Z0 (Drosophila simulans)
Explore B4Q3Z0 
Go to UniProtKB:  B4Q3Z0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4Q3Z0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.249 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.893α = 90
b = 46.893β = 90
c = 250.61γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references