6OPF

Crystal structure of dmNxf2 UBA domain fused with Panoramix helix

  • Classification: RNA BINDING PROTEIN
  • Organism(s): Drosophila melanogaster
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2019-04-24 Released: 2019-07-03 
  • Deposition Author(s): Wang, J., Patel, D.J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 6OKL


Literature

The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation.

Batki, J.Schnabl, J.Wang, J.Handler, D.Andreev, V.I.Stieger, C.E.Novatchkova, M.Lampersberger, L.Kauneckaite, K.Xie, W.Mechtler, K.Patel, D.J.Brennecke, J.

(2019) Nat Struct Mol Biol 26: 720-731

  • DOI: https://doi.org/10.1038/s41594-019-0270-6
  • Primary Citation of Related Structures:  
    6MRK, 6OPF

  • PubMed Abstract: 

    The PIWI-interacting RNA (piRNA) pathway protects genome integrity in part through establishing repressive heterochromatin at transposon loci. Silencing requires piRNA-guided targeting of nuclear PIWI proteins to nascent transposon transcripts, yet the subsequent molecular events are not understood. Here, we identify SFiNX (silencing factor interacting nuclear export variant), an interdependent protein complex required for Piwi-mediated cotranscriptional silencing in Drosophila. SFiNX consists of Nxf2-Nxt1, a gonad-specific variant of the heterodimeric messenger RNA export receptor Nxf1-Nxt1 and the Piwi-associated protein Panoramix. SFiNX mutant flies are sterile and exhibit transposon derepression because piRNA-loaded Piwi is unable to establish heterochromatin. Within SFiNX, Panoramix recruits heterochromatin effectors, while the RNA binding protein Nxf2 licenses cotranscriptional silencing. Our data reveal how Nxf2 might have evolved from an RNA transport receptor into a cotranscriptional silencing factor. Thus, NXF variants, which are abundant in metazoans, can have diverse molecular functions and might have been coopted for host genome defense more broadly.


  • Organizational Affiliation

    Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear RNA export factor 2, Panoramix fusionA,
B,
C [auth D],
D [auth F]
98Drosophila melanogasterMutation(s): 0 
Gene Names: nxf2CG4118PanxCG9754
UniProt
Find proteins for Q9VV73 (Drosophila melanogaster)
Explore Q9VV73 
Go to UniProtKB:  Q9VV73
Find proteins for Q9W2H9 (Drosophila melanogaster)
Explore Q9W2H9 
Go to UniProtKB:  Q9W2H9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9VV73Q9W2H9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.89α = 90
b = 72.89β = 109.9
c = 59.68γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
pointlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30 GM124165
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30 CA008748

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description