8U7B | pdb_00008u7b

Crystal structure of Apo form of Short Prokaryotic Argonaute TIR-APAZ (SPARTA) heterodimer

PDB DOI: https://doi.org/10.2210/pdb8U7B/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Thermoflavifilum thermophilum
Expression System: Escherichia coli, Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-09-15 Released: 2024-06-12
Deposition Author(s): Kottur, J., Aggarwal, A.K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.66 Å
R-Value Free:
0.239 (Depositor), 0.241 (DCC)
R-Value Work:
0.179 (Depositor), 0.189 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Nucleic acid mediated activation of a short prokaryotic Argonaute immune system.

Kottur, J., Malik, R., Aggarwal, A.K.

(2024) Nat Commun 15: 4852-4852

PubMed: 38844755 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-024-49271-4
Primary Citation Related Structures:
8U72, 8U7B

PubMed Abstract:
A short prokaryotic Argonaute (pAgo) TIR-APAZ (SPARTA) defense system, activated by invading DNA to unleash its TIR domain for NAD(P) ⁺ hydrolysis, was recently identified in bacteria. We report the crystal structure of SPARTA heterodimer in the absence of guide-RNA/target-ssDNA (2.66 Å) and a cryo-EM structure of the SPARTA oligomer (tetramer of heterodimers) bound to guide-RNA/target-ssDNA at nominal 3.15-3.35 Å resolution. The crystal structure provides a high-resolution view of SPARTA, revealing the APAZ domain as equivalent to the N, L1, and L2 regions of long pAgos and the MID domain containing a unique insertion (insert57). Cryo-EM structure reveals regions of the PIWI (loop10-9) and APAZ (helix αN) domains that reconfigure for nucleic-acid binding and decrypts regions/residues that reorganize to expose a positively charged pocket for higher-order assembly. The TIR domains amass in a parallel-strands arrangement for catalysis. We visualize SPARTA before and after RNA/ssDNA binding and uncover the basis of its active assembly leading to abortive infection.

Organizational Affiliation

Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. jitheshkottur@iav.res.in.

Macromolecule Content

Total Structure Weight: 112.36 kDa
Atom Count: 7,507
Modeled Residue Count: 931
Deposited Residue Count: 956
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TIR domain-containing protein	A [auth B]	449	Thermoflavifilum thermophilum	Mutation(s): 0 Gene Names: SAMN05660895_1670
UniProt
Find proteins for A0A1I7NFG5 (Thermoflavifilum thermophilum) Explore A0A1I7NFG5 Go to UniProtKB: A0A1I7NFG5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1I7NFG5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Piwi domain-containing protein	B [auth C]	507	Thermoflavifilum thermophilum	Mutation(s): 0 Gene Names: SAMN05660895_1671
UniProt
Find proteins for A0A1I7NFD7 (Thermoflavifilum thermophilum) Explore A0A1I7NFD7 Go to UniProtKB: A0A1I7NFD7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1I7NFD7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRO Query on PRO Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain J [auth C] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth B] SDF format, chain C [auth B] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth B] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth B]	C [auth B] D [auth B] E [auth B] F [auth B] G [auth B] C [auth B], D [auth B], E [auth B], F [auth B], G [auth B], J [auth C], K [auth C]	PROLINE C₅ H₉ N O₂ ONIBWKKTOPOVIA-BYPYZUCNSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain J [auth C] Focus chain K [auth C] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain J [auth C] Focus chain K [auth C]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain H [auth C] mmCIF format, chain I [auth C] mmCIF format, chain H [auth C]	H [auth C], I [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Focus chain I [auth C] Interactions & Density Focus chain H [auth C] Focus chain I [auth C]