6D9L

Ternary RsAgo Complex with Guide RNA and Target DNA Containing G-A Non-canonical Pair


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation 3D Report Full Report



Literature

Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA.

Liu, Y.Esyunina, D.Olovnikov, I.Teplova, M.Kulbachinskiy, A.Aravin, A.A.Patel, D.J.

(2018) Cell Rep 24: 453-462

  • DOI: 10.1016/j.celrep.2018.06.021
  • Primary Citation of Related Structures:  
    6D8F, 6D8A, 6D95, 6D92, 6D8P, 6D9L, 6D9K

  • PubMed Abstract: 
  • Prokaryotic Argonaute (Ago) proteins were recently shown to target foreign genetic elements, thus making them a perfect model for studies of interference mechanisms. Here, we study interactions of Rhodobacter sphaeroides Ago (RsAgo) with guide RNA (g ...

    Prokaryotic Argonaute (Ago) proteins were recently shown to target foreign genetic elements, thus making them a perfect model for studies of interference mechanisms. Here, we study interactions of Rhodobacter sphaeroides Ago (RsAgo) with guide RNA (gRNA) and fully complementary or imperfect target DNA (tDNA) using biochemical and structural approaches. We show that RsAgo can specifically recognize both the first nucleotide in gRNA and complementary nucleotide in tDNA, and both interactions contribute to nucleic acid binding. Non-canonical pairs and bulges on the target strand can be accommodated by RsAgo with minimal perturbation of the duplex but significantly reduce RsAgo affinity to tDNA. Surprisingly, mismatches between gRNA and tDNA induce dissociation of the guide-target duplex from RsAgo. Our results reveal plasticity in the ability of Ago proteins to accommodate helical imperfections, show how this might affect the efficiency of RNA silencing, and suggest a potential mechanism for guide release and Ago recycling.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address: pateld@mskcc.org.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinAF791Rhodobacter sphaeroides ATCC 17025Mutation(s): 0 
Gene Names: Rsph17025_3694
Find proteins for A4WYU7 (Rhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3))
Explore A4WYU7 
Go to UniProtKB:  A4WYU7
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*UP*UP*AP*CP*UP*GP*CP*GP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A)-3')C, H18Rhodobacter sphaeroides ATCC 17025
    Find similar nucleic acids by: 
    (by identity cutoff)  |  Structure
    Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*AP*GP*CP*AP*GP*TP*AP*AP*C)-3')G, J24Rhodobacter sphaeroides ATCC 17025
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MG
    Query on MG

    Download CCD File 
    C, H
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.60 Å
    • R-Value Free: 0.253 
    • R-Value Work: 0.212 
    • R-Value Observed: 0.214 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 68.045α = 90
    b = 118.253β = 95.51
    c = 117.827γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    PDB_EXTRACTdata extraction
    HKL-2000data reduction
    HKL-2000data scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2018-07-25
      Type: Initial release