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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: Li, Y. / Zheng, Q. / Jiang, Y. / Li, S.
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
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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