8IFK | pdb_00008ifk

Cryo-EM structure of monomeric SPARTA gRNA-ssDNA target complex

• PDB DOI: https://doi.org/10.2210/pdb8IFK/pdb
• EM Map EMD-35419: EMDB EMDataResource
• NAKB: 8IFK

• Classification: RNA BINDING PROTEIN/RNA/DNA
• Organism(s): Thermoflavifilum thermophilum, Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2023-02-18 Released: 2024-01-17 
• Deposition Author(s): Zhang, J.T., Jia, N.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.54 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Target ssDNA activates the NADase activity of prokaryotic SPARTA immune system.

Zhang, J.T., Wei, X.Y., Cui, N., Tian, R., Jia, N.

(2024) Nat Chem Biol 20: 503-511

• PubMed: 37932528 
• DOI: https://doi.org/10.1038/s41589-023-01479-z
• Primary Citation Related Structures: 
  8IFK, 8IFL, 8IFM, 8K34


• PubMed Abstract: 
  

  Argonaute proteins (Agos), which use small RNAs or DNAs as guides to recognize complementary nucleic acid targets, mediate RNA silencing in eukaryotes. In prokaryotes, Agos are involved in immunity: the short prokaryotic Ago/TIR-APAZ (SPARTA) immune system triggers cell death by degrading NAD ⁺ in response to invading plasmids, but its molecular mechanisms remain unknown. Here we used cryo-electron microscopy to determine the structures of inactive monomeric and active tetrameric Crenotalea thermophila SPARTA complexes, revealing mechanisms underlying SPARTA assembly, RNA-guided recognition of target single-stranded DNA (ssDNA) and subsequent SPARTA tetramerization, as well as tetramerization-dependent NADase activation. The small RNA guides Ago to recognize its ssDNA target, inducing SPARTA tetramerization via both Ago- and TIR-mediated interactions and resulting in a two-stranded, parallel, head-to-tail TIR rearrangement primed for NAD ⁺ hydrolysis. Our findings thus identify the molecular basis for target ssDNA-mediated SPARTA activation, which will facilitate the development of SPARTA-based biotechnological tools.

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Organizational Affiliation: 
• Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, China.
Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China. [e-mail].
Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, China. [e-mail].
Shenzhen Key Laboratory of Cell Microenvironment, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, China. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 125.93 kDa 
• Atom Count: 7,632 
• Modeled Residue Count: 864 
• Deposited Residue Count: 1,003 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TIR domain-containing protein	A	450	Thermoflavifilum thermophilum	Mutation(s): 0  Gene Names: SAMN05660895_1670
UniProt
Find proteins for A0A1I7NFG5 (Thermoflavifilum thermophilum) Explore A0A1I7NFG5  Go to UniProtKB:  A0A1I7NFG5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Piwi domain-containing protein	B	507	Thermoflavifilum thermophilum	Mutation(s): 0  Gene Names: SAMN05660895_1671
UniProt
Find proteins for A0A1I7NFD7 (Thermoflavifilum thermophilum) Explore A0A1I7NFD7  Go to UniProtKB:  A0A1I7NFD7

Entity ID: 3
Molecule	Chains	Length	Organism	Image
guide RNA	C	21	Escherichia coli 'BL21-Gold(DE3)pLysS AG

Entity ID: 4
Molecule	Chains	Length	Organism	Image
target ssDNA	D	25	Escherichia coli 'BL21-Gold(DE3)pLysS AG

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.54 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Zhang, J.T., Jia, N.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Database references
• Version 1.2: 2024-04-10
  Changes: Database references