Crystal structure of Drosophila Piwi

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 

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This is version 1.2 of the entry. See complete history


Crystal structure of Drosophila Piwi.

Yamaguchi, S.Oe, A.Nishida, K.M.Yamashita, K.Kajiya, A.Hirano, S.Matsumoto, N.Dohmae, N.Ishitani, R.Saito, K.Siomi, H.Nishimasu, H.Siomi, M.C.Nureki, O.

(2020) Nat Commun 11: 858-858

  • DOI: https://doi.org/10.1038/s41467-020-14687-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    PIWI-clade Argonaute proteins associate with PIWI-interacting RNAs (piRNAs), and silence transposons in animal gonads. Here, we report the crystal structure of the Drosophila PIWI-clade Argonaute Piwi in complex with endogenous piRNAs, at 2.9 Å resolution. A structural comparison of Piwi with other Argonautes highlights the PIWI-specific structural features, such as the overall domain arrangement and metal-dependent piRNA recognition. Our structural and biochemical data reveal that, unlike other Argonautes including silkworm Siwi, Piwi has a non-canonical DVDK tetrad and lacks the RNA-guided RNA cleaving slicer activity. Furthermore, we find that the Piwi mutant with the canonical DEDH catalytic tetrad exhibits the slicer activity and readily dissociates from less complementary RNA targets after the slicer-mediated cleavage, suggesting that the slicer activity could compromise the Piwi-mediated co-transcriptional silencing. We thus propose that Piwi lost the slicer activity during evolution to serve as an RNA-guided RNA-binding platform, thereby ensuring faithful co-transcriptional silencing of transposons.

  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein piwi810Drosophila melanogasterMutation(s): 0 
EC: 3.1.26
Find proteins for Q9VKM1 (Drosophila melanogaster)
Explore Q9VKM1 
Go to UniProtKB:  Q9VKM1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9VKM1
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
piRNA5Drosophila melanogaster
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HG (Subject of Investigation/LOI)
Query on HG

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
L [auth A]
M [auth A]
C [auth A],
D [auth A],
E [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.09α = 90
b = 115.64β = 90
c = 119.89γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
DIALSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description