6IEW

The crystal structure of the dNxf2 UBA domain in complex with Panoramix


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 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 ...

    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

    University of Chinese Academy of Sciences, Beijing, China. yuyang@ibp.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fusion protein of Nuclear RNA export factor 2 and Protein panoramixA94Drosophila 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.074α = 90
b = 40.925β = 90
c = 83.091γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data collection
Cootmodel building
PHENIXphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-09-17 
  • Released Date: 2019-08-21 
  • Deposition Author(s): Huang, Y., Cheng, S.

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: 2019-08-21
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references