2XDY

Crystal structure of the N. crassa QDE-2 AGO MID domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure and Ligand Binding of the Mid Domain of a Eukaryotic Argonaute Protein.

Boland, A.Tritschler, F.Heimstaedt, S.Izaurralde, E.Weichenrieder, O.

(2010) Embo Rep. 11: 522

  • DOI: 10.1038/embor.2010.81

  • PubMed Abstract: 
  • Argonaute (AGO) proteins are core components of RNA-induced silencing complexes and have essential roles in RNA-mediated gene silencing. They are characterized by a bilobal architecture, consisting of one lobe containing the amino-terminal and PAZ do ...

    Argonaute (AGO) proteins are core components of RNA-induced silencing complexes and have essential roles in RNA-mediated gene silencing. They are characterized by a bilobal architecture, consisting of one lobe containing the amino-terminal and PAZ domains and another containing the MID and PIWI domains. Except for the PAZ domain, structural information on eukaryotic AGO domains is not yet available. In this study, we report the crystal structure of the MID domain of the eukaryotic AGO protein QDE-2 from Neurospora crassa. This domain adopts a Rossmann-like fold and recognizes the 5'-terminal nucleotide of a guide RNA in a manner similar to its prokaryotic counterparts. The 5'-nucleotide-binding site shares common residues with a second, adjacent ligand-binding site, suggesting a mechanism for the cooperative binding of ligands to the MID domain of eukaryotic AGOs.


    Organizational Affiliation

    Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, Tübingen D-72076, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POST-TRANSCRIPTIONAL GENE SILENCING PROTEIN QDE-2
A
145Neurospora crassaMutation(s): 0 
Find proteins for Q9P8T1 (Neurospora crassa)
Go to UniProtKB:  Q9P8T1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.193 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 80.100α = 90.00
b = 91.390β = 90.00
c = 42.930γ = 90.00
Software Package:
Software NamePurpose
SHELXphasing
PHENIXrefinement
autoSHARPphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-16
    Type: Initial release
  • Version 1.1: 2011-05-19
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance