[English] 日本語
Yorodumi
- EMDB-61787: active NbaSPARDA complexes -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61787
Titleactive NbaSPARDA complexes
Map data
Sample
  • Complex: PRO-RNA-21DNA complex
    • Protein or peptide: Ago
    • Protein or peptide: DREN-APAZ
    • DNA: DNA (5'-D(*TP*AP*TP*CP*GP*TP*CP*AP*GP*CP*TP*GP*TP*GP*CP*AP*GP*TP*AP*TP*T)-3')
    • 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
Keywordsprotein / RNA / DNA / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA-DNA complex
Biological speciesNovosphingopyxis baekryungensis DSM 16222 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsZhuang L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Res / Year: 2025
Title: Target DNA-induced filament formation and nuclease activation of SPARDA complex.
Authors: Feng Wang / Haijiang Xu / Chendi Zhang / Jialin Xue / Zhuang Li /
Abstract: The short Argonaute-based bacterial defense system, SPARDA (Short Prokaryotic Argonaute and DNase/RNase-APAZ), utilizes guide RNA to target invading complementary DNA and exhibits collateral nuclease ...The short Argonaute-based bacterial defense system, SPARDA (Short Prokaryotic Argonaute and DNase/RNase-APAZ), utilizes guide RNA to target invading complementary DNA and exhibits collateral nuclease activity, leading to cell death or dormancy. However, its detailed mechanisms remain poorly understood. In this study, we investigated the SPARDA system from Novosphingopyxis baekryungensis (NbaSPARDA) and discovered an unexpected filament configuration upon target DNA binding, which strongly correlated with collateral nuclease activity. Filament formation and nuclease activation require a guide-target heteroduplex of sufficient length with perfect complementarity at the central region. A series of cryo-EM structures of NbaSPARDA complexes, loaded with guide RNA, target DNA of varying lengths, and substrate ssDNA, were determined at ~3.0 Å resolution. Structural analyses indicated that guide RNA binding induces dimerization of the NbaSPARDA complex, while target DNA engagement disrupts this dimerization. Further propagation of the guide-target heteroduplex triggers filament formation through a checkpoint mechanism. The NbaSPARDA filament consists of a backbone formed by interlocking short Argonaute proteins, with an inner layer composed of DREN nuclease domains. Filament formation leads to tetramerization of the monomeric DREN nuclease domain, activating its collateral nuclease activity against environmental nucleic acids - a feature leveraged for molecular diagnostics. For bacteria heterologously expressing the NbaSPARDA system, defense against invading bacteriophages and plasmids relies on filament formation. Collectively, these findings illustrate the detailed working mechanism of the NbaSPARDA complex and highlight the importance of its filament formation in host defense.
History
DepositionOct 1, 2024-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_61787.png

Downloads & links

-
Map

FileDownload / File: emd_61787.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 512 pix.
= 435.2 Å		0.85 Å/pix.
x 512 pix.
= 435.2 Å		0.85 Å/pix.
x 512 pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.5802434 - 1.2418791
Average (Standard dev.)0.0024521437 (±0.039893586)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_61787_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_61787_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : PRO-RNA-21DNA complex

EntireName: PRO-RNA-21DNA complex
Components
  • Complex: PRO-RNA-21DNA complex
    • Protein or peptide: Ago
    • Protein or peptide: DREN-APAZ
    • DNA: DNA (5'-D(*TP*AP*TP*CP*GP*TP*CP*AP*GP*CP*TP*GP*TP*GP*CP*AP*GP*TP*AP*TP*T)-3')
    • 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

-
Supramolecule #1: PRO-RNA-21DNA complex

SupramoleculeName: PRO-RNA-21DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Novosphingopyxis baekryungensis DSM 16222 (bacteria)

-
Macromolecule #1: Ago

MacromoleculeName: Ago / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Novosphingopyxis baekryungensis DSM 16222 (bacteria)
Molecular weightTheoretical: 54.492809 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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

-
Macromolecule #2: DREN-APAZ

MacromoleculeName: DREN-APAZ / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Novosphingopyxis baekryungensis DSM 16222 (bacteria)
Molecular weightTheoretical: 50.419645 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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

-
Macromolecule #3: DNA (5'-D(*TP*AP*TP*CP*GP*TP*CP*AP*GP*CP*TP*GP*TP*GP*CP*AP*GP*TP*...

MacromoleculeName: DNA (5'-D(*TP*AP*TP*CP*GP*TP*CP*AP*GP*CP*TP*GP*TP*GP*CP*AP*GP*TP*AP*TP*T)-3')
type: dna / ID: 3 / Number of copies: 4 / Classification: DNA
Source (natural)Organism: Novosphingopyxis baekryungensis DSM 16222 (bacteria)
Molecular weightTheoretical: 6.444168 KDa
SequenceString:
(DT)(DA)(DT)(DC)(DG)(DT)(DC)(DA)(DG)(DC) (DT)(DG)(DT)(DG)(DC)(DA)(DG)(DT)(DA)(DT) (DT)

-
Macromolecule #4: 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: 4 / Number of copies: 4
Source (natural)Organism: Novosphingopyxis baekryungensis DSM 16222 (bacteria)
Molecular weightTheoretical: 6.390879 KDa
SequenceString:
AUACUGCACA GCUGACGAUA

-
Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39659
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more