2W42

THE STRUCTURE OF A PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH A 16NT DNA DUPLEX.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Enhancement of the Seed-Target Recognition Step in RNA Silencing by a Piwi-Mid Domain Protein

Parker, J.S.Parizotto, E.A.Wang, M.Roe, S.M.Barford, D.

(2009) Mol.Cell 33: 204

  • DOI: 10.1016/j.molcel.2008.12.012

  • PubMed Abstract: 
  • Target recognition in RNA silencing is governed by the "seed sequence" of a guide RNA strand associated with the PIWI/MID domain of an Argonaute protein in RISC. Using a reconstituted in vitro target recognition system, we show that a model PIWI/MID ...

    Target recognition in RNA silencing is governed by the "seed sequence" of a guide RNA strand associated with the PIWI/MID domain of an Argonaute protein in RISC. Using a reconstituted in vitro target recognition system, we show that a model PIWI/MID domain protein confers position-dependent tightening and loosening of guide-strand-target interactions. Over the seed sequence, the interaction affinity is enhanced up to approximately 300-fold. Enhancement is achieved through a reduced entropy penalty for the interaction. In contrast, interactions 3' of the seed are inhibited. We quantified mismatched target recognition inside and outside the seed, revealing amplified discrimination at the third position in the seed mediated by the PIWI/MID domain. Thus, association of the guide strand with the PIWI/MID domain generates an enhanced affinity anchor site over the seed that can promote fidelity in target recognition and stabilize and guide the assembly of the active silencing complex.


    Organizational Affiliation

    Institute of Cancer Research, Chester Beatty Laboratories, London, UK. james.parker@bioch.ox.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE UNCHARACTERIZED PROTEIN
A, B
427Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)Mutation(s): 0 
Find proteins for O28951 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Go to UniProtKB:  O28951
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*TP*CP*GP*AP*CP*GP*CP)-3'P,R8Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*GP*TP*CP*GP*AP*AP*TP*TP)-3'Q,S8Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 51.838α = 75.80
b = 61.384β = 75.86
c = 103.540γ = 79.47
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance