1YVU

Crystal structure of A. aeolicus Argonaute


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of A. aeolicus Argonaute provides unique perspectives into the mechanism of guide strand-mediated mRNA cleavage

Yuan, Y.R.Pei, Y.Ma, J.B.Kuryavyi, V.Zhadina, M.Meister, G.Chen, H.Y.Dauter, Z.Tuschl, T.Patel, D.J.

(2005) Mol.Cell 19: 405-419

  • DOI: 10.1016/j.molcel.2005.07.011
  • Primary Citation of Related Structures:  2ADS

  • PubMed Abstract: 
  • Argonaute (Ago) proteins constitute a key component of the RNA-induced silencing complex (RISC). We report the crystal structure of Aquifex aeolicus Ago (Aa-Ago) together with binding and cleavage studies, which establish this eubacterial Ago as a bo ...

    Argonaute (Ago) proteins constitute a key component of the RNA-induced silencing complex (RISC). We report the crystal structure of Aquifex aeolicus Ago (Aa-Ago) together with binding and cleavage studies, which establish this eubacterial Ago as a bona fide guide DNA strand-mediated site-specific RNA endonuclease. We have generated a stereochemically robust model of the complex, where the guide DNA-mRNA duplex is positioned within a basic channel spanning the bilobal interface, such that the 5' phosphate of the guide strand can be anchored in a basic pocket, and the mRNA can be positioned for site-specific cleavage by RNase H-type divalent cation-coordinated catalytic Asp residues of the PIWI domain. Domain swap experiments involving chimeras of human Ago (hAgo1) and cleavage-competent hAgo2 reinforce the role of the PIWI domain in "slicer" activity. We propose a four-step Ago-mediated catalytic cleavage cycle model, which provides distinct perspectives into the mechanism of guide strand-mediated mRNA cleavage within the RISC.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
hypothetical protein aq_1447
A
706Aquifex aeolicus (strain VF5)N/A
Find proteins for O67434 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O67434
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.150α = 90.00
b = 100.679β = 90.00
c = 115.217γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
SHARPphasing
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-09
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance