3HJF

Crystal structure of T. thermophilus Argonaute E546 mutant protein complexed with DNA guide strand and 15-nt RNA target strand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.056 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes.

Wang, Y.Juranek, S.Li, H.Sheng, G.Wardle, G.S.Tuschl, T.Patel, D.J.

(2009) Nature 461: 754-761

  • DOI: 10.1038/nature08434
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The slicer activity of the RNA-induced silencing complex resides within its Argonaute (Ago) component, in which the PIWI domain provides the catalytic residues governing guide-strand mediated site-specific cleavage of target RNA. Here we report on st ...

    The slicer activity of the RNA-induced silencing complex resides within its Argonaute (Ago) component, in which the PIWI domain provides the catalytic residues governing guide-strand mediated site-specific cleavage of target RNA. Here we report on structures of ternary complexes of Thermus thermophilus Ago catalytic mutants with 5'-phosphorylated 21-nucleotide guide DNA and complementary target RNAs of 12, 15 and 19 nucleotides in length, which define the molecular basis for Mg(2+)-facilitated site-specific cleavage of the target. We observe pivot-like domain movements within the Ago scaffold on proceeding from nucleation to propagation steps of guide-target duplex formation, with duplex zippering beyond one turn of the helix requiring the release of the 3'-end of the guide from the PAZ pocket. Cleavage assays on targets of various lengths supported this model, and sugar-phosphate-backbone-modified target strands showed the importance of structural and catalytic divalent metal ions observed in the crystal structures.


    Organizational Affiliation

    Structural Biology Program, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Argonaute
A
685Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 1 
Find proteins for Q746M7 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q746M7
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3'X21N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-R(*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3'Y15N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
X
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.056 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.202 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 111.868α = 90.00
b = 111.868β = 90.00
c = 177.035γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
PHASERphasing
SCALEPACKdata scaling
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description