1W9H

The Structure of a Piwi protein from Archaeoglobus fulgidus.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal Structure of a Piwi Protein Suggests Mechanisms for Sirna Recognition and Slicer Activity

Parker, J.S., Roe, S.M., Barford, D.

(2004) EMBO J 23: 4727

  • DOI: 10.1038/sj.emboj.7600488
  • Primary Citation of Related Structures:  
    1W9H

  • PubMed Abstract: 

    • RNA silencing regulates gene expression through mRNA degradation, translation repression and chromatin remodelling. The fundamental engines of RNA silencing are RISC and RITS complexes, whose common components are 21-25 nt RNA and an Argonaute protein containing a PIWI domain of unknown function ...

    RNA silencing regulates gene expression through mRNA degradation, translation repression and chromatin remodelling. The fundamental engines of RNA silencing are RISC and RITS complexes, whose common components are 21-25 nt RNA and an Argonaute protein containing a PIWI domain of unknown function. The crystal structure of an archaeal Piwi protein (AfPiwi) is organised into two domains, one resembling the sugar-binding portion of the lac repressor and another with similarity to RNase H. Invariant residues and a coordinated metal ion lie in a pocket that surrounds the conserved C-terminus of the protein, defining a key functional region in the PIWI domain. Furthermore, two Asp residues, conserved in the majority of Argonaute sequences, align spatially with the catalytic Asp residues of RNase H-like catalytic sites, suggesting that in eukaryotic Argonaute proteins the RNase H-like domain may possess nuclease activity. The conserved region around the C-terminus of the PIWI domain, which is required for small interfering RNA (siRNA) binding to AfPiwi, may function as the receptor site for the obligatory 5' phosphate of siRNAs, thereby specifying the cleavage position of the target mRNA.

    Organizational Affiliation: 

    Section of Structural Biology, The Institute of Cancer Research, Chester Beatty Laboratories, London, UK.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYPOTHETICAL PROTEIN AF1318A427Archaeoglobus fulgidusMutation(s): 0 
Find proteins for O28951 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Explore O28951 
Go to UniProtKB:  O28951
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
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A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N		 Ligand Interaction
NI
Query on NI
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A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N		 Ligand Interaction
CL
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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.09α = 90
b = 137.863β = 90
c = 51.663γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
SHARPphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-13
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-05
    Changes: Refinement description