5I4A

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.949 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A bacterial Argonaute with noncanonical guide RNA specificity.

Kaya, E.Doxzen, K.W.Knoll, K.R.Wilson, R.C.Strutt, S.C.Kranzusch, P.J.Doudna, J.A.

(2016) Proc.Natl.Acad.Sci.USA 113: 4057-4062

  • DOI: 10.1073/pnas.1524385113

  • PubMed Abstract: 
  • Eukaryotic Argonaute proteins induce gene silencing by small RNA-guided recognition and cleavage of mRNA targets. Although structural similarities between human and prokaryotic Argonautes are consistent with shared mechanistic properties, sequence an ...

    Eukaryotic Argonaute proteins induce gene silencing by small RNA-guided recognition and cleavage of mRNA targets. Although structural similarities between human and prokaryotic Argonautes are consistent with shared mechanistic properties, sequence and structure-based alignments suggested that Argonautes encoded within CRISPR-cas [clustered regularly interspaced short palindromic repeats (CRISPR)-associated] bacterial immunity operons have divergent activities. We show here that the CRISPR-associated Marinitoga piezophila Argonaute (MpAgo) protein cleaves single-stranded target sequences using 5'-hydroxylated guide RNAs rather than the 5'-phosphorylated guides used by all known Argonautes. The 2.0-Å resolution crystal structure of an MpAgo-RNA complex reveals a guide strand binding site comprising residues that block 5' phosphate interactions. Using structure-based sequence alignment, we were able to identify other putative MpAgo-like proteins, all of which are encoded within CRISPR-cas loci. Taken together, our data suggest the evolution of an Argonaute subclass with noncanonical specificity for a 5'-hydroxylated guide.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Argonaute protein
A, C
642Marinitoga piezophila (strain DSM 14283 / JCM 11233 / KA3)N/A
Find proteins for H2J4R4 (Marinitoga piezophila (strain DSM 14283 / JCM 11233 / KA3))
Go to UniProtKB:  H2J4R4
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*U)-3')B,D21synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.949 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.216 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 50.883α = 110.87
b = 75.420β = 90.55
c = 102.215γ = 90.09
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2016-04-13
    Type: Database references
  • Version 1.2: 2016-06-15
    Type: Database references
  • Version 1.3: 2016-07-06
    Type: Data collection