9IIZ

Cryo-EM Structure of EfPiwi-piRNA-target (25-nt, comma)

• PDB DOI: https://doi.org/10.2210/pdb9IIZ/pdb
• NAKB: 9IIZ
• EM Map EMD-60610: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Ephydatia fluviatilis, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-06-21 Released: 2024-11-13 
• Deposition Author(s): Li, Z.Q., Xu, Q.K., Wu, J.P., Shen, E.Z.
• Funding Organization(s): Other private

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Experimental Data Snapshot

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

Literature

Structural insights into RNA cleavage by PIWI Argonaute

Li, Z.Q., Xu, Q.K., Wu, J.P., Shen, E.Z.

(2024) Nature 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 126.23 kDa 
• Atom Count: 4,080 
• Modelled Residue Count: 426 
• Deposited Residue Count: 1,036 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Piwi	A	987	Ephydatia fluviatilis	Mutation(s): 0  Gene Names: EfPiwiA
UniProt
Find proteins for D5MRY8 (Ephydatia fluviatilis) Explore D5MRY8  Go to UniProtKB:  D5MRY8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (25-MER)	B	25	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*GP*CP*CP*AP*AP*GP*UP*UP*UP*CP*CP*AP*UP*GP*UP*UP*GP*AP*UP*GP*GP*UP*A)-3')	C	24	Homo sapiens

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-13 
Deposition Author(s): Li, Z.Q., Xu, Q.K., Wu, J.P., Shen, E.Z.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2024-11-13
  Type: Initial release