1Z26 | pdb_00001z26

Structure of Pyrococcus furiosus Argonaute with bound tungstate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.282 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.217 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1Z26

This is version 1.5 of the entry. See complete history

Literature

Purified Argonaute2 and an siRNA form recombinant human RISC.

Rivas, F.V.Tolia, N.H.Song, J.J.Aragon, J.P.Liu, J.Hannon, G.J.Joshua-Tor, L.

(2005) Nat Struct Mol Biol 12: 340-349

  • DOI: https://doi.org/10.1038/nsmb918
  • Primary Citation Related Structures: 
    1Z25, 1Z26

  • PubMed Abstract: 

    Genetic, biochemical and structural studies have implicated Argonaute proteins as the catalytic core of the RNAi effector complex, RISC. Here we show that recombinant, human Argonaute2 can combine with a small interfering RNA (siRNA) to form minimal RISC that accurately cleaves substrate RNAs. Recombinant RISC shows many of the properties of RISC purified from human or Drosophila melanogaster cells but also has surprising features. It shows no stimulation by ATP, suggesting that factors promoting product release are missing from the recombinant enzyme. The active site is made up of a unique Asp-Asp-His (DDH) motif. In the RISC reconstitution system, the siRNA 5' phosphate is important for the stability and the fidelity of the complex but is not essential for the creation of an active enzyme. These studies demonstrate that Argonaute proteins catalyze mRNA cleavage within RISC and provide a source of recombinant enzyme for detailed biochemical studies of the RNAi effector complex.


  • Organizational Affiliation
    • Cold Spring Harbor Laboratory, Watson School of Biological Sciences, New York 11724, USA.

Macromolecule Content 

  • Total Structure Weight: 91.34 kDa 
  • Atom Count: 6,106 
  • Modeled Residue Count: 716 
  • Deposited Residue Count: 771 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Argonaute771Pyrococcus furiosusMutation(s): 1 
EC: 3.1.24
UniProt
Find proteins for Q8U3D2 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U3D2 
Go to UniProtKB:  Q8U3D2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U3D2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.282 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.217 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.1α = 90
b = 103.501β = 102.46
c = 73.225γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-02-14
    Changes: Data collection