Crystal structure of Aa-Ago with externally-bound siRNA

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.209 

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A Potential Protein-RNA Recognition Event along the RISC-Loading Pathway from the Structure of A. aeolicus Argonaute with Externally Bound siRNA.

Yuan, Y.R.Pei, Y.Chen, H.Y.Tuschl, T.Patel, D.J.

(2006) Structure 14: 1557-1565

  • DOI: https://doi.org/10.1016/j.str.2006.08.009
  • Primary Citation of Related Structures:  
    2F8S, 2F8T

  • PubMed Abstract: 

    Argonaute proteins are key components of the RNA-induced silencing complex (RISC). They provide both architectural and catalytic functionalities associated with small interfering RNA (siRNA) guide strand recognition and subsequent guide strand-mediated cleavage of complementary mRNAs. We report on the 3.0 A crystal structures of 22-mer and 26-mer siRNAs bound to Aquifex aeolicus Argonaute (Aa-Ago), where one 2 nt 3' overhang of the siRNA inserts into a cavity positioned on the outer surface of the PAZ-containing lobe of the bilobal Aa-Ago architecture. The first overhang nucleotide stacks over a tyrosine ring, while the second overhang nucleotide, together with the intervening sugar-phosphate backbone, inserts into a preformed surface cavity. Photochemical crosslinking studies on Aa-Ago with 5-iodoU-labeled single-stranded siRNA and siRNA duplex provide support for this externally bound siRNA-Aa-Ago complex. The structure and biochemical data together provide insights into a protein-RNA recognition event potentially associated with the RISC-loading pathway.

  • Organizational Affiliation

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


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Argonaute proteinC [auth A],
D [auth B]
706Aquifex aeolicusMutation(s): 0 
Find proteins for O67434 (Aquifex aeolicus (strain VF5))
Explore O67434 
Go to UniProtKB:  O67434
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67434
Sequence Annotations
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
26-MERA [auth C],
B [auth D]
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.2α = 90
b = 118.077β = 99.57
c = 98.498γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-31
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Refinement description