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

Target-induced Argonaute-HNH filaments confer bacterial immunity

Murakami, K.S., Narwal, M., Kanevskaya, A., Kulbachinskiy, A.

To be published.

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