6IHJ

Crystal structure of Drosophila Nxf1 NTF2 domain in complex with Nxt1/p15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Pandas complex adapted for piRNA-guided transcriptional silencing and heterochromatin formation.

Zhao, K.Cheng, S.Miao, N.Xu, P.Lu, X.Zhang, Y.Wang, M.Ouyang, X.Yuan, X.Liu, W.Lu, X.Zhou, P.Gu, J.Zhang, Y.Qiu, D.Jin, Z.Su, C.Peng, C.Wang, J.H.Dong, M.Q.Wan, Y.Ma, J.Cheng, H.Huang, Y.Yu, Y.

(2019) Nat Cell Biol 21: 1261-1272

  • DOI: https://doi.org/10.1038/s41556-019-0396-0
  • Primary Citation of Related Structures:  
    6IEW, 6IHJ

  • PubMed Abstract: 

    The repression of transposons by the Piwi-interacting RNA (piRNA) pathway is essential to protect animal germ cells. In Drosophila, Panoramix enforces transcriptional silencing by binding to the target-engaged Piwi-piRNA complex, although the precise mechanisms by which this occurs remain elusive. Here, we show that Panoramix functions together with a germline-specific paralogue of a nuclear export factor, dNxf2, and its cofactor dNxt1 (p15), to suppress transposon expression. The transposon RNA-binding protein dNxf2 is required for animal fertility and Panoramix-mediated silencing. Transient tethering of dNxf2 to nascent transcripts leads to their nuclear retention. The NTF2 domain of dNxf2 competes dNxf1 (TAP) off nucleoporins, a process required for proper RNA export. Thus, dNxf2 functions in a Panoramix-dNxf2-dependent TAP/p15 silencing (Pandas) complex that counteracts the canonical RNA exporting machinery and restricts transposons to the nuclear peripheries. Our findings may have broader implications for understanding how RNA metabolism modulates heterochromatin formation.


  • Organizational Affiliation

    Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear RNA export factor 1A,
B [auth C]
191Drosophila melanogasterMutation(s): 0 
Gene Names: sbrnxf1CG1664
UniProt
Find proteins for Q9U1H9 (Drosophila melanogaster)
Explore Q9U1H9 
Go to UniProtKB:  Q9U1H9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9U1H9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NTF2-related export proteinC [auth B],
D
135Drosophila melanogasterMutation(s): 0 
Gene Names: Nxt1CG12752
UniProt
Find proteins for Q9V3H8 (Drosophila melanogaster)
Explore Q9V3H8 
Go to UniProtKB:  Q9V3H8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V3H8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.228 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.204α = 90
b = 152.204β = 90
c = 49.83γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina91640102
National Natural Science Foundation of ChinaChina31870741

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description