8OZI

cryoEM structure of SPARTA complex pre-NAD cleavage


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.22 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Activation mechanism of a short argonaute-TIR prokaryotic immune system.

Ni, D.Lu, X.Stahlberg, H.Ekundayo, B.

(2023) Sci Adv 9: eadh9002-eadh9002

  • DOI: https://doi.org/10.1126/sciadv.adh9002
  • Primary Citation of Related Structures:  
    8OZ6, 8OZC, 8OZD, 8OZE, 8OZF, 8OZG, 8OZI

  • PubMed Abstract: 

    Short prokaryotic argonaute (pAgo) and toll/interleukin-1 receptor/resistance protein (TIR)-analog of PAZ (APAZ) form a heterodimeric SPARTA complex that provides immunity to its prokaryotic host through an abortive infection mechanism. Monomeric SPARTA senses foreign RNA/DNA duplexes to assemble an active tetramer resulting in cell death by nicotinamide adenine dinucleotide (oxidized form) (NAD) depletion via an unknown mechanism. We report nine structures of SPARTA in different functional states at a resolution range of 4.2 to 2.9 angstroms, revealing its activation mechanism. Inactive SPARTA monomers bind to RNA/DNA duplexes to form symmetric dimers mediated by the association of Ago subunits. The initiation of tetramer assembly induces flexibility of the TIR domains enabling a symmetry-breaking rotational movement of a TIR domain in the dimer units which facilitates the TIR oligomerization, resulting in the formation of the substrate binding pocket and the activation of the SPARTA complex's NADase activity. Our findings provide detailed structural and mechanistic insights into activating a short argonaute defense system.


  • Organizational Affiliation

    Laboratory of Biological Electron Microscopy, IPHYS, SB, EPFL, and Dept. Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, Cubotron, Rt. de la Sorge, 1015 Lausanne, Switzerland.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TIR domain-containing proteinA,
E [auth C],
I [auth E],
K [auth G]
452Maribacter polysiphoniaeMutation(s): 0 
Gene Names: LX92_01810
UniProt
Find proteins for A0A316E683 (Maribacter polysiphoniae)
Explore A0A316E683 
Go to UniProtKB:  A0A316E683
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A316E683
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Piwi domain-containing proteinB,
F [auth D],
J [auth F],
L [auth H]
507Maribacter polysiphoniaeMutation(s): 0 
Gene Names: LX92_01809
UniProt
Find proteins for A0A316E3U6 (Maribacter polysiphoniae)
Explore A0A316E3U6 
Go to UniProtKB:  A0A316E3U6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A316E3U6
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')C [auth I],
G [auth K],
M,
N
18Maribacter polysiphoniae
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')D [auth J],
H [auth L],
O,
P
16Maribacter polysiphoniae
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.22 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandCRSII5_177195
Swiss National Science FoundationSwitzerlandIZLCZ0_206089

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release
  • Version 1.1: 2023-08-23
    Changes: Database references