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- PDB-9vx1: The cryo-EM structure of gRNA-bound SPARDA complex -

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Basic information

Entry
Database: PDB / ID: 9vx1
TitleThe cryo-EM structure of gRNA-bound SPARDA complex
Components
  • DREN-APAZ
  • RNA (5'-R(P*AP*UP*AP*CP*UP*GP*CP*AP*CP*AP*GP*CP*UP*GP*AP*CP*GP*AP*UP*A)-3')
  • pAgo
KeywordsCELL INVASION / Cryo-EM / pAgo / DREN-APAZ
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesNovosphingopyxis baekryungensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsLi, Y. / Jiang, Y. / Zheng, Q. / Li, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: Filament assembly induced by the recognition of target DNA activates the prokaryotic Argonaute SPARDA system.
Authors: Wanyue Zhang / Yuchen Jiang / Yu Li / Xiangkai Zhen / Shuying Xu / Ning-Shao Xia / Shaowei Li / Xurong Wang / Qingbing Zheng / Songying Ouyang /
Abstract: The short prokaryotic Argonaute (pAgo) proteins, in conjunction with their associated effector molecules, constitute a defence mechanism in prokaryotes that protects against phage infections. The ...The short prokaryotic Argonaute (pAgo) proteins, in conjunction with their associated effector molecules, constitute a defence mechanism in prokaryotes that protects against phage infections. The SPARDA is characterized by its collateral nuclease activity, which, upon activation through target DNA recognition, non-specifically cleaves a wide range of nucleic acid substrates. Nevertheless, the structural underpinnings of its collateral activity have remained elusive. In this study, we investigate the NbaSPARDA system from Novosphingopyxis baekryungensis and reveal that RNA-guided DNA recognition triggers the assembly of a higher-order filamentous structure. This filamentation is essential for the tetramerization of the DREN nuclease domain, which in turn facilitates the accumulation and cleavage of substrate nucleic acids. Through the determination of the gRNA-bound and RNA-DNA duplex-bound cryo-EM structures, we delineate a sequential monomer-dimer-monomer-filament transition during SPARDA activation. These insights collectively elucidate a filament-dependent activation mechanism underpinning the short pAgo-mediated immune response, which is crucial for antiviral defence.
History
DepositionJul 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: pAgo
B: DREN-APAZ
Z: RNA (5'-R(P*AP*UP*AP*CP*UP*GP*CP*AP*CP*AP*GP*CP*UP*GP*AP*CP*GP*AP*UP*A)-3')
D: pAgo
E: DREN-APAZ
a: RNA (5'-R(P*AP*UP*AP*CP*UP*GP*CP*AP*CP*AP*GP*CP*UP*GP*AP*CP*GP*AP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,6558
Polymers222,6076
Non-polymers492
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein pAgo


Mass: 54492.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingopyxis baekryungensis (bacteria)
Production host: Bacteria Latreille et al. 1825 (Bacteria stick insect)
#2: Protein DREN-APAZ


Mass: 50419.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingopyxis baekryungensis (bacteria)
Production host: Bacteria Latreille et al. 1825 (Bacteria stick insect)
#3: RNA chain RNA (5'-R(P*AP*UP*AP*CP*UP*GP*CP*AP*CP*AP*GP*CP*UP*GP*AP*CP*GP*AP*UP*A)-3')


Mass: 6390.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingopyxis baekryungensis (bacteria)
Production host: Novosphingopyxis baekryungensis (bacteria)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: The structure of gRNA-bound SPARDA complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Novosphingopyxis baekryungensis (bacteria)
Source (recombinant)Organism: Bacteria Latreille et al. 1825 (Bacteria stick insect)
Buffer solutionpH: 7.4
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98314 / Symmetry type: POINT

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