2XDY

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

• PDB DOI: https://doi.org/10.2210/pdb2XDY/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Neurospora crassa
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2010-05-10 Released: 2010-06-16 
• Deposition Author(s): Boland, A., Tritschler, F., Weichenrieder, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.223 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

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

• PubMed: 20539312 
• DOI: https://doi.org/10.1038/embor.2010.81
• Primary Citation of Related Structures:  
  2XDY


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 16.26 kDa 
• Atom Count: 1,057 
• Modelled Residue Count: 127 
• Deposited Residue Count: 145 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POST-TRANSCRIPTIONAL GENE SILENCING PROTEIN QDE-2	A	145	Neurospora crassa	Mutation(s): 0
UniProt
Find proteins for Q9P8T1 (Neurospora crassa) Explore Q9P8T1  Go to UniProtKB:  Q9P8T1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.223 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.1	α = 90
b = 91.39	β = 90
c = 42.93	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
SHELX	phasing
autoSHARP	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-16 
Deposition Author(s): Boland, A., Tritschler, F., Weichenrieder, O.

Revision History  

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