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- PDB-9vx6: Helical structure of gRNA-tDNA SPARDA complex -

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Basic information

Entry
Database: PDB / ID: 9vx6
TitleHelical structure of gRNA-tDNA SPARDA complex
Components
  • DREN-APAZ
  • guide RNA
  • pAGO
  • substrate ssDNA
  • substrate ssRNA
  • target DNA
KeywordsCELL INVASION / Cryo-EM / SPARDA / pAgo
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciesBacteriophage sp. (virus)
Novosphingopyxis baekryungensis (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsLi, Y. / Zheng, Q. / Li, S. / Jiang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
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
Revision 1.0Jan 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Jan 14, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Jan 21, 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: target DNA
R: guide RNA
S: pAGO
T: DREN-APAZ
E: target DNA
F: guide RNA
I: target DNA
J: guide RNA
Q: target DNA
M: substrate ssDNA
N: substrate ssRNA
O: pAGO
P: DREN-APAZ
V: guide RNA
W: pAGO
Y: DREN-APAZ
U: pAGO
X: DREN-APAZ


Theoretical massNumber of molelcules
Total (without water)476,60418
Polymers476,60418
Non-polymers00
Water00
1


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

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Components

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DNA chain , 2 types, 5 molecules LEIQM

#1: DNA chain
target DNA


Mass: 6139.976 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage sp. (virus) / Production host: Bacteriophage sp. (virus)
#5: DNA chain substrate ssDNA


Mass: 3364.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage sp. (virus) / Production host: Bacteriophage sp. (virus)

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RNA chain , 2 types, 5 molecules RFJVN

#2: RNA chain
guide RNA


Mass: 6390.879 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingopyxis baekryungensis (bacteria)
Production host: Novosphingopyxis baekryungensis (bacteria)
#6: RNA chain substrate ssRNA


Mass: 3466.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingopyxis baekryungensis (bacteria)
Production host: Novosphingopyxis baekryungensis (bacteria)

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Protein , 2 types, 8 molecules SOWUTPYX

#3: Protein
pAGO


Mass: 54492.809 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingopyxis baekryungensis (bacteria)
Production host: Novosphingopyxis baekryungensis (bacteria)
#4: Protein
DREN-APAZ


Mass: 50419.645 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingopyxis baekryungensis (bacteria)
Production host: Bacteria Latreille et al. 1825 (Bacteria stick insect)

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: gRNA-tDNA SPARDA complex / Type: COMPLEX / Entity ID: all / 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
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.13_2998:model refinement
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 80 ° / Axial rise/subunit: 130 Å / Axial symmetry: C1
3D reconstructionResolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57938 / Symmetry type: HELICAL

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