5UX0

X-ray crystal structure of Marinitoga piezophila Argonaute in complex with 5' OH guide RNA and target DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.197 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

DNA recognition by an RNA-guided bacterial Argonaute.

Doxzen, K.W.Doudna, J.A.

(2017) PLoS ONE 12: e0177097-e0177097

  • DOI: 10.1371/journal.pone.0177097

  • PubMed Abstract: 
  • Argonaute (Ago) proteins are widespread in prokaryotes and eukaryotes and share a four-domain architecture capable of RNA- or DNA-guided nucleic acid recognition. Previous studies identified a prokaryotic Argonaute protein from the eubacterium Marini ...

    Argonaute (Ago) proteins are widespread in prokaryotes and eukaryotes and share a four-domain architecture capable of RNA- or DNA-guided nucleic acid recognition. Previous studies identified a prokaryotic Argonaute protein from the eubacterium Marinitoga piezophila (MpAgo), which binds preferentially to 5'-hydroxylated guide RNAs and cleaves single-stranded RNA (ssRNA) and DNA (ssDNA) targets. Here we present a 3.2 Å resolution crystal structure of MpAgo bound to a 21-nucleotide RNA guide and a complementary 21-nucleotide ssDNA substrate. Comparison of this ternary complex to other target-bound Argonaute structures reveals a unique orientation of the N-terminal domain, resulting in a straight helical axis of the entire RNA-DNA heteroduplex through the central cleft of the protein. Additionally, mismatches introduced into the heteroduplex reduce MpAgo cleavage efficiency with a symmetric profile centered around the middle of the helix. This pattern differs from the canonical mismatch tolerance of other Argonautes, which display decreased cleavage efficiency for substrates bearing sequence mismatches to the 5' region of the guide strand. This structural analysis of MpAgo bound to a hybrid helix advances our understanding of the diversity of target recognition mechanisms by Argonaute proteins.


    Organizational Affiliation

    Biophysics Graduate Group, University of California, Berkeley, California, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Argonaute protein
A, D
642Marinitoga piezophila (strain DSM 14283 / JCM 11233 / KA3)N/A
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
MacAB-like efflux pump, Spr0694-0695 section
Find proteins for H2J4R4 (Marinitoga piezophila (strain DSM 14283 / JCM 11233 / KA3))
Go to UniProtKB:  H2J4R4
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*G*GP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*AP*U)-3')B,E21synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*CP*C)-3')C,F21synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.197 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 85.003α = 90.00
b = 130.993β = 90.00
c = 171.468γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-06-07
    Type: Database references