6KR6 | pdb_00006kr6

Crystal structure of Drosophila Piwi

• PDB DOI: https://doi.org/10.2210/pdb6KR6/pdb
• NAKB: 6KR6

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2019-08-21 Released: 2020-02-19 
• Deposition Author(s): Yamaguchi, S., Oe, A., Yamashita, K., Hirano, S., Mastumoto, N., Ishitani, R., Nishimasu, H., Nureki, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.259 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 32051406 
• DOI: https://doi.org/10.1038/s41467-020-14687-1
• Primary Citation Related Structures: 
  6KR6


• 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.

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Organizational Affiliation: 
• Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
Invertebrate Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.
Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. [e-mail].
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan. [e-mail].
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 96.84 kDa 
• Atom Count: 5,504 
• Modeled Residue Count: 718 
• Deposited Residue Count: 815 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein piwi	A	810	Drosophila melanogaster	Mutation(s): 0  EC: 3.1.26
UniProt
Find proteins for Q9VKM1 (Drosophila melanogaster) Explore Q9VKM1  Go to UniProtKB:  Q9VKM1

Entity ID: 2
Molecule	Chains	Length	Organism	Image
piRNA	B	5	Drosophila melanogaster

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG (Subject of Investigation/LOI)	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.259 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Diffraction Data: https://doi.org/10.5281/zenodo.3603539

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.09	α = 90
b = 115.64	β = 90
c = 119.89	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
DIALS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-19 
Deposition Author(s): Yamaguchi, S., Oe, A., Yamashita, K., Hirano, S., Mastumoto, N., Ishitani, R., Nishimasu, H., Nureki, O.

Revision History  

• 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