5FIS

Exonuclease domain-containing 1 (Exd1) in the Gd bound conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Piwi Slicing and Exd1 Drive Biogenesis of Nuclear Pirnas from Cytosolic Targets of the Mouse Pirna Pathway

Yang, Z.Chen, K.M.Pandey, R.R.Homolka, D.Reuter, M.Rodino Janeiro, B.K.Sachidanandam, R.Fauvarque, M.O.Mccarthy, A.A.Pillai, R.S.

(2016) Mol.Cell 61: 138

  • DOI: 10.1016/j.molcel.2015.11.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • PIWI-interacting RNAs (piRNAs) guide PIWI proteins to suppress transposons in the cytoplasm and nucleus of animal germ cells, but how silencing in the two compartments is coordinated is not known. Here we demonstrate that endonucleolytic slicing of a ...

    PIWI-interacting RNAs (piRNAs) guide PIWI proteins to suppress transposons in the cytoplasm and nucleus of animal germ cells, but how silencing in the two compartments is coordinated is not known. Here we demonstrate that endonucleolytic slicing of a transcript by the cytosolic mouse PIWI protein MILI acts as a trigger to initiate its further 5'→3' processing into non-overlapping fragments. These fragments accumulate as new piRNAs within both cytosolic MILI and the nuclear MIWI2. We also identify Exonuclease domain-containing 1 (EXD1) as a partner of the MIWI2 piRNA biogenesis factor TDRD12. EXD1 homodimers are inactive as a nuclease but function as an RNA adaptor within a PET (PIWI-EXD1-Tdrd12) complex. Loss of Exd1 reduces sequences generated by MILI slicing, impacts biogenesis of MIWI2 piRNAs, and de-represses LINE1 retrotransposons. Thus, piRNA biogenesis triggered by PIWI slicing, and promoted by EXD1, ensures that the same guides instruct PIWI proteins in the nucleus and cytoplasm.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EXD1
A
243Bombyx moriMutation(s): 0 
Gene Names: EXD1
Find proteins for H9IUR0 (Bombyx mori)
Go to Gene View: EXD1
Go to UniProtKB:  H9IUR0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
EXD1
B
243Bombyx moriMutation(s): 0 
Gene Names: EXD1
Find proteins for H9IUR0 (Bombyx mori)
Go to Gene View: EXD1
Go to UniProtKB:  H9IUR0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GD
Query on GD

Download SDF File 
Download CCD File 
A, B
GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A, B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.157 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 82.860α = 90.00
b = 135.700β = 90.00
c = 51.460γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SHELXphasing
BUCCANEERphasing
SHARPphasing
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2016-01-13
    Type: Database references
  • Version 1.2: 2016-01-20
    Type: Database references