4F1N

Crystal structure of Kluyveromyces polysporus Argonaute with a guide RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.187 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of yeast Argonaute with guide RNA.

Nakanishi, K.Weinberg, D.E.Bartel, D.P.Patel, D.J.

(2012) Nature 486: 368-374

  • DOI: 10.1038/nature11211

  • PubMed Abstract: 
  • The RNA-induced silencing complex, comprising Argonaute and guide RNA, mediates RNA interference. Here we report the 3.2 Å crystal structure of Kluyveromyces polysporus Argonaute (KpAGO) fortuitously complexed with guide RNA originating from small-RN ...

    The RNA-induced silencing complex, comprising Argonaute and guide RNA, mediates RNA interference. Here we report the 3.2 Å crystal structure of Kluyveromyces polysporus Argonaute (KpAGO) fortuitously complexed with guide RNA originating from small-RNA duplexes autonomously loaded by recombinant KpAGO. Despite their diverse sequences, guide-RNA nucleotides 1-8 are positioned similarly, with sequence-independent contacts to bases, phosphates and 2'-hydroxyl groups pre-organizing the backbone of nucleotides 2-8 in a near-A-form conformation. Compared with prokaryotic Argonautes, KpAGO has numerous surface-exposed insertion segments, with a cluster of conserved insertions repositioning the N domain to enable full propagation of guide-target pairing. Compared with Argonautes in inactive conformations, KpAGO has a hydrogen-bond network that stabilizes an expanded and repositioned loop, which inserts an invariant glutamate into the catalytic pocket. Mutation analyses and analogies to ribonuclease H indicate that insertion of this glutamate finger completes a universally conserved catalytic tetrad, thereby activating Argonaute for RNA cleavage.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
KpAGO
A, B
1046Vanderwaltozyma polyspora (strain ATCC 22028 / DSM 70294)Mutation(s): 0 
Find proteins for A7TMA9 (Vanderwaltozyma polyspora (strain ATCC 22028 / DSM 70294))
Go to UniProtKB:  A7TMA9
Entity ID: 2
MoleculeChainsLengthOrganism
RNA 5'-R(P*UP*AP*AP*AP*AP*AP*AP*AP*A)-3'E,F9Vanderwaltozyma polyspora DSM 70294
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.187 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.168 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 171.553α = 90.00
b = 171.553β = 90.00
c = 83.177γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
SHELXSphasing
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2012-07-04
    Type: Database references