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)

Macromolecule Content

• Total Structure Weight: 43.17 kDa 
• Atom Count: 3065 
• Modelled Residue Count: 368 
• Deposited Residue Count: 388 
• Unique protein chains: 1

2YHA

Crystal Structure of the N. crassa QDE-2 AGO MID-PIWI Domains

• PDB DOI: 10.2210/pdb2YHA/pdb

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


• Deposited: 2011-04-27 Released: 2011-06-15 
• Deposition Author(s): Boland, A., Weichenrieder, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.236 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 

Literature

Crystal Structure of the Mid-Piwi Lobe of a Eukaryotic Argonaute Protein

Boland, A., Huntzinger, E., Schmidt, S., Izaurralde, E., Weichenriede, O.

(2011) Proc Natl Acad Sci U S A 108: 10466

• PubMed: 21646546 
• DOI: 10.1073/pnas.1103946108
• Primary Citation of Related Structures:  
  2YHA, 2YHB


• PubMed Abstract: 
  

Argonaute proteins (AGOs) are essential effectors in RNA-mediated gene silencing pathways. They are characterized by a bilobal architecture, in which one lobe contains the N-terminal and PAZ domains and the other contains the MID and PIWI domains. Here, we present the first crystal structure of the MID-PIWI lobe from a eukaryotic AGO, the Neurospora crassa QDE-2 protein. Compared to prokaryotic AGOs, the domain orientation is conserved, indicating a conserved mode of nucleic acid binding. The PIWI domain shows an adaptable surface loop next to a eukaryote-specific α-helical insertion, which are both likely to contact the PAZ domain in a conformation-dependent manner to sense the functional state of the protein. The MID-PIWI interface is hydrophilic and buries residues that were previously thought to participate directly in the allosteric regulation of guide RNA binding. The interface includes the binding pocket for the guide RNA 5' end, and residues from both domains contribute to binding. Accordingly, micro-RNA (miRNA) binding is particularly sensitive to alteration in the MID-PIWI interface in Drosophila melanogaster AGO1 in vivo. The structure of the QDE-2 MID-PIWI lobe provides molecular and mechanistic insight into eukaryotic AGOs and has significant implications for understanding the role of these proteins in silencing.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POST-TRANSCRIPTIONAL GENE SILENCING PROTEIN QDE-2	A	388	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]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.236 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.08	α = 90
b = 63.08	β = 90
c = 170.47	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-04-27 
• Released Date: 2011-06-15 
Deposition Author(s): Boland, A., Weichenrieder, O.

Revision History  

• Version 1.0: 2011-06-15
  Type: Initial release
  
• Version 1.1: 2011-06-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance