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- EMDB-65405: The cryo-EM structure of gRNA-bound SPARDA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-65405
TitleThe cryo-EM structure of gRNA-bound SPARDA complex
Map dataThe main map of gRNA-bound SPARDA
Sample
  • Complex: The structure of gRNA-bound SPARDA complex
    • Protein or peptide: pAgo
    • Protein or peptide: DREN-APAZ
    • RNA: 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')
  • Ligand: MAGNESIUM ION
KeywordsCryo-EM / pAgo / DREN-APAZ / CELL INVASION
Biological speciesNovosphingopyxis baekryungensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsLi Y / Jiang Y / Zheng Q / Li S
Funding support1 items
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, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65405.png

Downloads & links

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Map

FileDownload / File: emd_65405.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe main map of gRNA-bound SPARDA
Voxel sizeX=Y=Z: 0.65 Å
Density
Contour LevelBy AUTHOR: 0.128
Minimum - Maximum-0.0017955991 - 2.2180116
Average (Standard dev.)0.0015280028 (±0.029121852)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 249.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: The local map of gRNA-bound SPARDA

Fileemd_65405_additional_1.map
AnnotationThe local map of gRNA-bound SPARDA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half map of gRNA-bound SPARDA

Fileemd_65405_half_map_1.map
AnnotationThe half map of gRNA-bound SPARDA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half map of gRNA-bound SPARDA

Fileemd_65405_half_map_2.map
AnnotationThe half map of gRNA-bound SPARDA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The structure of gRNA-bound SPARDA complex

EntireName: The structure of gRNA-bound SPARDA complex
Components
  • Complex: The structure of gRNA-bound SPARDA complex
    • Protein or peptide: pAgo
    • Protein or peptide: DREN-APAZ
    • RNA: 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')
  • Ligand: MAGNESIUM ION

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Supramolecule #1: The structure of gRNA-bound SPARDA complex

SupramoleculeName: The structure of gRNA-bound SPARDA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Novosphingopyxis baekryungensis (bacteria)

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Macromolecule #1: pAgo

MacromoleculeName: pAgo / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Novosphingopyxis baekryungensis (bacteria)
Molecular weightTheoretical: 54.492809 KDa
Recombinant expressionOrganism: Bacteria Latreille et al. 1825 (Bacteria stick insect)
SequenceString: MTFETRIFDE PELEFGDHHH HQDPRLGLSE AGPLQTFLGD VIKIGVVGNS KTIEDTRKFI ETVSSGVEGK GEKHPNMHPP FPGLGNQSP YRCRFEIEDG ATAALTKSKL DKIGKEPDHY RAVEMAVDEI IGELQAMDDG GSRPDVAIIA LPVKLLERVW N AKVDARGT ...String:
MTFETRIFDE PELEFGDHHH HQDPRLGLSE AGPLQTFLGD VIKIGVVGNS KTIEDTRKFI ETVSSGVEGK GEKHPNMHPP FPGLGNQSP YRCRFEIEDG ATAALTKSKL DKIGKEPDHY RAVEMAVDEI IGELQAMDDG GSRPDVAIIA LPVKLLERVW N AKVDARGT TEKSDSSGSD APNFRGMLKA KAMGLSFPIQ IVWEDVIDDK VTIPQKVKES SSRKIQDIAG RTWNLMTSLY YK GSGRIPW RRMPLEGEFS ACYVGISFYR EADGQQLFTS AAQMFDERGR GFVLKGRRAR TESRGRHPYM AREDAKKIIE DVL AAYKLH HKTLPARVFI LKTSRFKDEE ADGIIAALDE AGTELRDLVW VQESYTARIL RDGNYPVLRG TFVDLHGKGL LYTS GSMPY YGTYPGKYDP NPLLLCPHHT SESTVAQLAE EIFSLTKVNW NSTQMNQRLP IPIRAARKVG EVLKYVGEGE VISAD YRKY I

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Macromolecule #2: DREN-APAZ

MacromoleculeName: DREN-APAZ / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Novosphingopyxis baekryungensis (bacteria)
Molecular weightTheoretical: 50.419645 KDa
Recombinant expressionOrganism: Bacteria Latreille et al. 1825 (Bacteria stick insect)
SequenceString: MTKKITANQI IGEIGENEVR GRFLTLGWQF DGRSRLEAGI DGIAEVMNEG QPMARMIAVQ IKSTKEGKYT SESDTSFTYL LRTQDLAYW RGSNLPVIVV FYRQSDHSFY WKEVSRDAGP GERRLNIDKV ADLFNASTVN KLAALTVPKT GLGYYVPPLG G GEDALINM ...String:
MTKKITANQI IGEIGENEVR GRFLTLGWQF DGRSRLEAGI DGIAEVMNEG QPMARMIAVQ IKSTKEGKYT SESDTSFTYL LRTQDLAYW RGSNLPVIVV FYRQSDHSFY WKEVSRDAGP GERRLNIDKV ADLFNASTVN KLAALTVPKT GLGYYVPPLG G GEDALINM LPLTLPNEMY IASTTYEPRK AIAVILNGDG PKRFDWVING GTFWSFHDPR TSACSEIVDI DQVEAINTKE LA LHDDIDE QNRFSHLLRQ TLRYQTDSDL GWDKDHKALY FRAIEREVSR NFAYTSSKKK TDANVVSVFK NSKDETRVSF VRH HAFSPR FELMADQWYL IITPTYYYTT NGYAPHQFAA PLLAGKKRLD KSAALRGQVI MWHRFLTQSD HEDLFHSEET PEAY LMFGE PPSIHLDVRV PEDGWVKEKV KRIDEAAQGE GLFSDDI

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Macromolecule #3: RNA (5'-R(P*AP*UP*AP*CP*UP*GP*CP*AP*CP*AP*GP*CP*UP*GP*AP*CP*GP*AP...

MacromoleculeName: 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')
type: rna / ID: 3 / Number of copies: 2
Source (natural)Organism: Novosphingopyxis baekryungensis (bacteria)
Molecular weightTheoretical: 6.390879 KDa
SequenceString:
AUACUGCACA GCUGACGAUA

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 98314
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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