Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 96.31 kDa 
• Atom Count: 5,828 
• Modelled Residue Count: 736 
• Deposited Residue Count: 793 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 7KX7

Cryo-EM structure of Ephydatia fluviatilis PiwiA-piRNA complex

• PDB DOI:  https://doi.org/10.2210/pdb7KX7/pdb
• EM Map EMD-23061: EMDB EMDataResource

• Classification: HYDROLASE,RNA BINDING PROTEIN/RNA
• Organism(s): Ephydatia fluviatilis, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2020-12-03 Released: 2021-07-14 
• Deposition Author(s): Anzelon, T.A., Chowdhury, S., Lander, G.C., MacRae, I.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for piRNA targeting.

Anzelon, T.A., Chowdhury, S., Hughes, S.M., Xiao, Y., Lander, G.C., MacRae, I.J.

(2021) Nature 597: 285-289

• PubMed: 34471284 
• DOI: https://doi.org/10.1038/s41586-021-03856-x
• Primary Citation of Related Structures:  
  7KX7, 7KX9


• PubMed Abstract: 
  

PIWI proteins use PIWI-interacting RNAs (piRNAs) to identify and silence transposable elements and thereby maintain genome integrity between metazoan generations ¹ . The targeting of transposable elements by PIWI has been compared to mRNA target recognition by Argonaute proteins ^2,3 , which use microRNA (miRNA) guides, but the extent to which piRNAs resemble miRNAs is not known. Here we present cryo-electron microscopy structures of a PIWI-piRNA complex from the sponge Ephydatia fluviatilis with and without target RNAs, and a biochemical analysis of target recognition. Mirroring Argonaute, PIWI identifies targets using the piRNA seed region. However, PIWI creates a much weaker seed so that stable target association requires further piRNA-target pairing, making piRNAs less promiscuous than miRNAs. Beyond the seed, the structure of PIWI facilitates piRNA-target pairing in a manner that is tolerant of mismatches, leading to long-lived PIWI-piRNA-target interactions that may accumulate on transposable-element transcripts. PIWI ensures targeting fidelity by physically blocking the propagation of piRNA-target interactions in the absence of faithful seed pairing, and by requiring an extended piRNA-target duplex to reach an endonucleolytically active conformation. PIWI proteins thereby minimize off-targeting cellular mRNAs while defending against evolving genomic threats.

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Organizational Affiliation: 

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Piwi-A	A	768	Ephydatia fluviatilis	Mutation(s): 0  Gene Names: EfPiwiA EC: 3.1.26
UniProt
Find proteins for D5MRY8 (Ephydatia fluviatilis) Explore D5MRY8  Go to UniProtKB:  D5MRY8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*CP*UP*CP*AP*GP*(OMC))-3')	B	25	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Anzelon, T.A., Chowdhury, S., Lander, G.C., MacRae, I.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2021-07-14
  Type: Initial release
  
• Version 1.1: 2021-09-01
  Changes: Database references
• Version 1.2: 2021-09-15
  Changes: Database references
• Version 1.3: 2021-09-22
  Changes: Database references