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- EMDB-37490: Focused map for area 1 of MapSPARTA tetramer bound with guide-target -

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Basic information

Entry
Database: EMDB / ID: EMD-37490
TitleFocused map for area 1 of MapSPARTA tetramer bound with guide-target
Map dataFocused on area 1
Sample
  • Complex: Maribacter polysiphoniae short Ago complexed with TIR-APAZ
    • DNA: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*AP*GP*U)-3')
    • DNA: DNA (25-MER)
    • Protein or peptide: Piwi domain-containing protein
    • Protein or peptide: TIR domain-containing protein
KeywordsSPARTA / Ago / Tir / DNA BINDING PROTEIN/DNA/RNA / DNA BINDING PROTEIN-DNA-RNA complex
Biological speciesMaribacter polysiphoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHuang PP / Li ZX / Guo LJ / Xiao YB / Chen MR
Funding support China, 5 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)Nos.2018YFA0902000 China
Ministry of Science and Technology (MoST, China)ZX-2021ZD0203404 China
National Natural Science Foundation of China (NSFC)Nos. 32271330 China
National Natural Science Foundation of China (NSFC)Nos. 32000889 China
National Natural Science Foundation of China (NSFC)Nos. 31970547 China
CitationJournal: Biochem Biophys Res Commun / Year: 2026
Title: Structural and functional characterization of SPARTA system.
Authors: Hongze Zhao / Pingping Huang / Lijie Guo / Xinning Jiang / Zhaoxing Li / Bingjie Tao / Meiling Lu / Lianwen Qi / Lei Zhang / Yibei Xiao / Meirong Chen /
Abstract: Short prokaryotic Argonaute associated with TIR-APAZ (SPARTA) is a bacterial defense system that oligomerizes to activate the TIR domain, depleting NAD upon guide-mediated target DNA recognition. ...Short prokaryotic Argonaute associated with TIR-APAZ (SPARTA) is a bacterial defense system that oligomerizes to activate the TIR domain, depleting NAD upon guide-mediated target DNA recognition. Previous studies have shown a marked activity divergence between thermophilic Crenotalea thermophila SPARTA (CrtSPARTA) and Maribacter polysiphoniae SPARTA (MapSPARTA); however, the underlying mechanism remains unclear. Here, through biochemical and structural analysis, we found that compared with the relatively rigid CrtSPARTA, MapSPARTA exhibits much more flexibility in its TIR domain, which flips during the formation of active tetramers. Interestingly, we found that the activity of CrtSPARTA, but not MapSPARTA, could be significantly enhanced when we weakened the interaction between the MID and TIR domains by introducing mutations at the interface, suggesting that the MID-TIR interaction restricts the release of CrtTIR and thus the activation of CrtSPARTA. Following guide-target recognition, this flexibility-induced activation can be further promoted by higher temperatures within the physiological range or Ca, together suggesting that the restriction of TIR by the MID-TIR interaction may be a strategy to prevent auto-activation of thermophilic CrtSPARTA. Meanwhile, we also found that tRNA fragments can serve as guide RNAs for SPARTA activation, which probably reveals the origin of the RNA guide for prokaryotic Argonaute. This also suggests the possibility that SPARTA may function cooperatively with other defense systems involving a tRNA endonuclease to efficiently respond to viral infection.
History
DepositionSep 19, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37490.png

Downloads & links

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Map

FileDownload / File: emd_37490.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused on area 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 384 pix.
= 403.2 Å		1.05 Å/pix.
x 384 pix.
= 403.2 Å		1.05 Å/pix.
x 384 pix.
= 403.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.48815805 - 0.9325067
Average (Standard dev.)-0.0003632925 (±0.012664007)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 403.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37490_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37490_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Maribacter polysiphoniae short Ago complexed with TIR-APAZ

EntireName: Maribacter polysiphoniae short Ago complexed with TIR-APAZ
Components
  • Complex: Maribacter polysiphoniae short Ago complexed with TIR-APAZ
    • DNA: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*AP*GP*U)-3')
    • DNA: DNA (25-MER)
    • Protein or peptide: Piwi domain-containing protein
    • Protein or peptide: TIR domain-containing protein

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Supramolecule #1: Maribacter polysiphoniae short Ago complexed with TIR-APAZ

SupramoleculeName: Maribacter polysiphoniae short Ago complexed with TIR-APAZ
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Maribacter polysiphoniae (bacteria)

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Macromolecule #1: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP...

MacromoleculeName: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*AP*GP*U)-3')
type: dna / ID: 1 / Details: guide RNA / Classification: DNA
Source (natural)Organism: Maribacter polysiphoniae (bacteria)
SequenceString:
UGACGGCUCU AAUCUAUUAG U

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Macromolecule #2: DNA (25-MER)

MacromoleculeName: DNA (25-MER) / type: dna / ID: 2
Details: (DC)(DA)(DA)(DC)(DT)(DA)(DA)(DT)(DA)(DG)(DA)(DT)(DT)(DA)(DG)(DA)(DG)(DC)(DC)(DG) (DT)(DC)(DA)(DA)(DT)
Classification: DNA
Source (natural)Organism: Maribacter polysiphoniae (bacteria)
SequenceString:
(DC)(DA)(DA)(DC)(DT)(DA)(DA)(DT)(DA)(DG) (DA)(DT)(DT)(DA)(DG)(DA)(DG)(DC)(DC)(DG) (DT)(DC)(DA)(DA)(DT)

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Macromolecule #3: Piwi domain-containing protein

MacromoleculeName: Piwi domain-containing protein / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Maribacter polysiphoniae (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKELIYIEEP KILFAHGQKC TDARDGLALF GPLNNLYGIK SGVIGTKQGL KIFRDYLDHI QKPIYNSNSI TRPMFPGFEA VFDCKWEST GITFKEVTNE DIGKFLYNSS THKRTYDLVS LFIDKIISAN KNEDENVDVW FVIVPDEIYK YCRPNSVLPK E MVQTKALM ...String:
MKELIYIEEP KILFAHGQKC TDARDGLALF GPLNNLYGIK SGVIGTKQGL KIFRDYLDHI QKPIYNSNSI TRPMFPGFEA VFDCKWEST GITFKEVTNE DIGKFLYNSS THKRTYDLVS LFIDKIISAN KNEDENVDVW FVIVPDEIYK YCRPNSVLPK E MVQTKALM SKSKAKSFRY EPSLFPDINI ELKEQEKEAE TYNYDAQFHD QFKARLLKHT IPTQIFREST LAWRDFKNAF GL PIRDFSK IEGHLAWTIS TAAFYKAGGK PWKLSDVRNG VCYLGLVYKK VEKSKNPRNA CCAAQMFLDN GDGTVFKGEV GPW YNPKNG QYHLEPKEAK ALLSQSLQSY KEQIGEYPKE VFIHAKTRFN HQEWDAFLEV TPKETNLVGV TISKTKPLKL YKTE GDYTI LRGNAYVVNE RSAFLWTVGY VPKIQTALSM EVPNPLFIEI NKGEADIKQV LKDILSLTKL NYNACIFADG EPVTL RFAD KIGEILTAST DIKTPPLAFK YYI

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Macromolecule #4: TIR domain-containing protein

MacromoleculeName: TIR domain-containing protein / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Maribacter polysiphoniae (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRNKIFISHA TPDDNDFTRW LALKLIGLGY EVWCDILFLD KGVDFWSNIE KVIREDTCKF LLVSSSYSNQ REGVLKELAV AAKVKKQLK DDKFIIPLAI DEQLSYDDIN IDIVRLNAID FKMSWARGLK DILEAFEKQK VPKEVADASK SNLLYQQIFL H DKSVIEKE ...String:
MRNKIFISHA TPDDNDFTRW LALKLIGLGY EVWCDILFLD KGVDFWSNIE KVIREDTCKF LLVSSSYSNQ REGVLKELAV AAKVKKQLK DDKFIIPLAI DEQLSYDDIN IDIVRLNAID FKMSWARGLK DILEAFEKQK VPKEVADASK SNLLYQQIFL H DKSVIEKE EIYDSNWLSI LSFPEELRFH EYNWMLPKRF DVRELTFPAV RYKNYLCTFA WAYDFTYHLP KTETYHKSKT IR IPTEEIL SGSYDSNFIR NAECKRLIVQ LLNKAFELRM KDKEVQEYEM SNKTAYWLEK GKLEKDKFEK TMLVGKQKDK NWH FAISGA SKLYPFPVLM ISSHIFFTAD GKKLIDSSSV QHSSRRRQGK NWWNNTWRTK LLAFIKYLSD DDTSFYLEMG SEEK VFVSN EPVKFKGNVS YNIPEKNTLE EEAELSGFNQ GEDIEELEEL IENLEAE

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 183347
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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