Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 10.34 kDa 
• Atom Count: 951 
• Modelled Residue Count: 91 
• Deposited Residue Count: 94 
• Unique protein chains: 1

6IEW

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

• PDB DOI: 10.2210/pdb6IEW/pdb

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


• Deposited: 2018-09-17 Released: 2019-08-21 
• Deposition Author(s): Huang, Y., Cheng, S.
• Funding Organization(s): National Natural Science Foundation of China

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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 

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

• PubMed: 31570835 
• 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. 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.

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Organizational Affiliation: 

University of Chinese Academy of Sciences, Beijing, China. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion protein of Nuclear RNA export factor 2 and Protein panoramix	A	94	Drosophila melanogaster	Mutation(s): 0  Gene Names: nxf2, CG4118, Panx, CG9754
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
UniProt Groups	Q9VV73Q9W2H9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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 = 29.074	α = 90
b = 40.925	β = 90
c = 83.091	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
Coot	model building
PHENIX	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	91640102
National Natural Science Foundation of China	China	31870741

Revision History  

• Version 1.0: 2019-08-21
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Database references