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- PDB-8wp2: MapSPARTA tetramer bound with guide-target -

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Basic information

Entry
Database: PDB / ID: 8wp2
TitleMapSPARTA tetramer bound with guide-target
Components
  • DNA (25-MER)
  • Piwi domain-containing protein
  • RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*AP*GP*U)-3')
  • TIR domain-containing protein
KeywordsRNA BINDING PROTEIN/DNA/RNA / SPARTA / Ago / Tir / RNA BINDING PROTEIN-DNA-RNA complex
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciesMaribacter polysiphoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHuang, P.P. / Li, Z.X. / Guo, L.J. / Xiao, Y.B. / Chen, M.R.
Funding support China, 5items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)Nos.2018YFA0902000 China
Ministry of Science and Technology (MoST, China)ZX-2021ZD0203404 China
National Natural Science Foundation of China (NSFC)Nos. 32271330 China
National Natural Science Foundation of China (NSFC)Nos. 32000889 China
National Natural Science Foundation of China (NSFC)Nos. 31970547 China
CitationJournal: Biochem Biophys Res Commun / Year: 2026
Title: Structural and functional characterization of SPARTA system.
Authors: Hongze Zhao / Pingping Huang / Lijie Guo / Xinning Jiang / Zhaoxing Li / Bingjie Tao / Meiling Lu / Lianwen Qi / Lei Zhang / Yibei Xiao / Meirong Chen /
Abstract: Short prokaryotic Argonaute associated with TIR-APAZ (SPARTA) is a bacterial defense system that oligomerizes to activate the TIR domain, depleting NAD upon guide-mediated target DNA recognition. ...Short prokaryotic Argonaute associated with TIR-APAZ (SPARTA) is a bacterial defense system that oligomerizes to activate the TIR domain, depleting NAD upon guide-mediated target DNA recognition. Previous studies have shown a marked activity divergence between thermophilic Crenotalea thermophila SPARTA (CrtSPARTA) and Maribacter polysiphoniae SPARTA (MapSPARTA); however, the underlying mechanism remains unclear. Here, through biochemical and structural analysis, we found that compared with the relatively rigid CrtSPARTA, MapSPARTA exhibits much more flexibility in its TIR domain, which flips during the formation of active tetramers. Interestingly, we found that the activity of CrtSPARTA, but not MapSPARTA, could be significantly enhanced when we weakened the interaction between the MID and TIR domains by introducing mutations at the interface, suggesting that the MID-TIR interaction restricts the release of CrtTIR and thus the activation of CrtSPARTA. Following guide-target recognition, this flexibility-induced activation can be further promoted by higher temperatures within the physiological range or Ca, together suggesting that the restriction of TIR by the MID-TIR interaction may be a strategy to prevent auto-activation of thermophilic CrtSPARTA. Meanwhile, we also found that tRNA fragments can serve as guide RNAs for SPARTA activation, which probably reveals the origin of the RNA guide for prokaryotic Argonaute. This also suggests the possibility that SPARTA may function cooperatively with other defense systems involving a tRNA endonuclease to efficiently respond to viral infection.
History
DepositionOct 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.0Dec 11, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 11, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 11, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name
Revision 1.2Jul 29, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.2Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Piwi domain-containing protein
B: TIR domain-containing protein
C: Piwi domain-containing protein
D: TIR domain-containing protein
E: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*AP*GP*U)-3')
F: DNA (25-MER)
G: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*AP*GP*U)-3')
H: DNA (25-MER)
I: Piwi domain-containing protein
J: TIR domain-containing protein
K: Piwi domain-containing protein
L: TIR domain-containing protein
M: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*AP*GP*U)-3')
N: DNA (25-MER)
O: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*AP*GP*U)-3')
P: DNA (25-MER)


Theoretical massNumber of molelcules
Total (without water)502,75616
Polymers502,75616
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Piwi domain-containing protein


Mass: 58091.410 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Maribacter polysiphoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein
TIR domain-containing protein


Mass: 53270.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Maribacter polysiphoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: RNA chain
RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*AP*GP*U)-3')


Mass: 6651.949 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Maribacter polysiphoniae (bacteria)
#4: DNA chain
DNA (25-MER)


Mass: 7675.000 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Maribacter polysiphoniae (bacteria)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Maribacter polysiphoniae short Ago complexed with TIR-APAZ
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Maribacter polysiphoniae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 183347 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00932615
ELECTRON MICROSCOPYf_angle_d0.73244700
ELECTRON MICROSCOPYf_dihedral_angle_d16.4585299
ELECTRON MICROSCOPYf_chiral_restr0.0434859
ELECTRON MICROSCOPYf_plane_restr0.0065130

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