9OM4 | pdb_00009om4

Cryo-EM structure of filament form Acidithiobacillus caldus (Aca) short prokaryotic argonautes, HNH-associated (SPARHA) with gRNA and tDNA

• PDB DOI: https://doi.org/10.2210/pdb9OM4/pdb
• NAKB: 9OM4
• EM Map EMD-70606: EMDB EMDataResource

• Classification: IMMUNE SYSTEM/DNA/RNA
• Organism(s): Acidithiobacillus caldus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-05-13 Released: 2025-10-22 
• Deposition Author(s): Murakami, K.S., Narwal, M.
• 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: 3.38 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Argonaute-HNH filaments triggered by invader DNA confer bacterial immunity.

Kanevskaya, A., Narwal, M., Lisitskaya, L., Moiseenko, A.V., Sokolova, O.S., Sluchanko, N.N., Murakami, K.S., Kulbachinskiy, A.

(2025) Nat Commun 16: 11389-11389

• PubMed: 41315870 
• DOI: https://doi.org/10.1038/s41467-025-66189-7
• Primary Citation Related Structures: 
  9OM4


• PubMed Abstract: 
  

  Argonaute proteins provide innate immunity in all domains of life through guide-dependent recognition and cleavage of invader nucleic acids. Many short prokaryotic Argonautes (pAgos) lack nuclease activity and are instead co-encoded with tentative nuclease effectors, but their activation mechanisms remain unknown. Here, we characterize SPARHA systems (short prokaryotic argonautes, HNH-associated), containing HNH nuclease effectors. RNA-guided target DNA recognition by pAgo induces formation of SPARHA filaments with a chain of double nuclease sites formed by HNH tetramers, leading to indiscriminate collateral degradation of DNA and protecting bacterial population from invaders. We show that the assembly of filaments proceeds via a universal activation pathway involving a cascade of target-induced conformational changes in SPARHA, conserved in other short pAgo systems containing various types of effectors. pAgos and associated effectors act as modular defense systems that translate recognition of specific DNA into immune response through assembly of supramolecular complexes, deleterious for invaders and potentially useful for biotechnology.

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Organizational Affiliation: 
• Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia. [e-mail].
Department of Biochemistry and Molecular Biology, Huck Institutes of the Life Sciences, the Center for Structural Biology and the Center for RNA biology, Pennsylvania State University, University Park, PA, USA.
Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.
A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: electron microscopy

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Biological Assembly Evidence: electron microscopy

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors.

Biological Assembly Evidence: electron microscopy

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 5 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 458.71 kDa 
• Atom Count: 26,980 
• Modeled Residue Count: 3,120 
• Deposited Residue Count: 3,768 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HNH endonuclease	A, E, I, M	435	Acidithiobacillus caldus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Prokaryotic argonaute MID-PIWI family protein	B, F, J, N	471	Acidithiobacillus caldus	Mutation(s): 0
UniProt
Find proteins for A0A5B9QQE2 (Roseimaritima ulvae) Explore A0A5B9QQE2  Go to UniProtKB:  A0A5B9QQE2

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*UP*UP*UP*GP*GP*UP*UP*GP*CP*GP*GP*UP*GP*CP*UP*CP*U)-3')	C, G, K, O	18	Acidithiobacillus caldus

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*AP*GP*CP*AP*CP*CP*GP*CP*AP*AP*CP*CP*AP*AP*AP*T)-3')	D, H, L, P	18	Acidithiobacillus caldus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	Q [auth B], R [auth F], S [auth J], T [auth N]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.38 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.6.2
RECONSTRUCTION	cryoSPARC	4.6.2
MODEL REFINEMENT	PHENIX	dev_5330

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Murakami, K.S., Narwal, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM156623

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release
  
• Version 1.1: 2026-05-13
  Changes: Data collection, Database references