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- EMDB-41358: Structure of activated SAVED-CHAT filament -

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Basic information

Entry
Database: EMDB / ID: EMD-41358
TitleStructure of activated SAVED-CHAT filament
Map data
Sample
  • Complex: Active SAVED-CHAT filament
    • Protein or peptide: CHAT domain-containing protein
    • RNA: RNA (5'-R(*AP*AP*A)-3')
KeywordsSAVED-CHAT / IMMUNE SYSTEM
Function / homologySMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain / CHAT domain / CHAT domain / CHAT domain-containing protein
Function and homology information
Biological speciesHaliangium ochraceum (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBravo JPK / Taylor DW
Funding support United States, 2 items
OrganizationGrant numberCountry
Welch FoundationF-1938 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM138348 United States
CitationJournal: Science / Year: 2024
Title: Type III-B CRISPR-Cas cascade of proteolytic cleavages.
Authors: Jurre A Steens / Jack P K Bravo / Carl Raymund P Salazar / Caglar Yildiz / Afonso M Amieiro / Stephan Köstlbacher / Stijn H P Prinsen / Ane S Andres / Constantinos Patinios / Andreas Bardis ...Authors: Jurre A Steens / Jack P K Bravo / Carl Raymund P Salazar / Caglar Yildiz / Afonso M Amieiro / Stephan Köstlbacher / Stijn H P Prinsen / Ane S Andres / Constantinos Patinios / Andreas Bardis / Arjan Barendregt / Richard A Scheltema / Thijs J G Ettema / John van der Oost / David W Taylor / Raymond H J Staals /
Abstract: The generation of cyclic oligoadenylates and subsequent allosteric activation of proteins that carry sensory domains is a distinctive feature of type III CRISPR-Cas systems. In this work, we ...The generation of cyclic oligoadenylates and subsequent allosteric activation of proteins that carry sensory domains is a distinctive feature of type III CRISPR-Cas systems. In this work, we characterize a set of associated genes of a type III-B system from that contains two caspase-like proteases, SAVED-CHAT and PCaspase (prokaryotic caspase), co-opted from a cyclic oligonucleotide-based antiphage signaling system (CBASS). Cyclic tri-adenosine monophosphate (AMP)-induced oligomerization of SAVED-CHAT activates proteolytic activity of the CHAT domains, which specifically cleave and activate PCaspase. Subsequently, activated PCaspase cleaves a multitude of proteins, which results in a strong interference phenotype in vivo in Taken together, our findings reveal how a CRISPR-Cas-based detection of a target RNA triggers a cascade of caspase-associated proteolytic activities.
History
DepositionJul 26, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41358.png

Downloads & links

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Map

FileDownload / File: emd_41358.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 512 pix.
= 481.28 Å		0.94 Å/pix.
x 512 pix.
= 481.28 Å		0.94 Å/pix.
x 512 pix.
= 481.28 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.3386657 - 0.85621977
Average (Standard dev.)-0.00021213805 (±0.018346453)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 481.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41358_msk_1.map
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Additional map: Sharpened map

Fileemd_41358_additional_1.map
AnnotationSharpened map
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Half map: #1

Fileemd_41358_half_map_1.map
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Half map: #2

Fileemd_41358_half_map_2.map
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Sample components

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Entire : Active SAVED-CHAT filament

EntireName: Active SAVED-CHAT filament
Components
  • Complex: Active SAVED-CHAT filament
    • Protein or peptide: CHAT domain-containing protein
    • RNA: RNA (5'-R(*AP*AP*A)-3')

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Supramolecule #1: Active SAVED-CHAT filament

SupramoleculeName: Active SAVED-CHAT filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Haliangium ochraceum (bacteria)
Molecular weightTheoretical: 1.33 MDa

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Macromolecule #1: CHAT domain-containing protein

MacromoleculeName: CHAT domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Haliangium ochraceum (bacteria)
Molecular weightTheoretical: 54.378332 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: IQCILVLDLS IDNAITACSV TPHLPRAARR VELHLNDFGA ERAPYGGASD RRTWRCWMQA VDAMLADARA QLGAEVEFTH YYLAGRAAL PVFAYLGLRL GKQANITTVN RRDDGCWDVV PCQRPASSAA SGVSPSARFF DEVRGLDTDE RSSESGMVAV W VSTQRDVD ...String:
IQCILVLDLS IDNAITACSV TPHLPRAARR VELHLNDFGA ERAPYGGASD RRTWRCWMQA VDAMLADARA QLGAEVEFTH YYLAGRAAL PVFAYLGLRL GKQANITTVN RRDDGCWDVV PCQRPASSAA SGVSPSARFF DEVRGLDTDE RSSESGMVAV W VSTQRDVD RGLLRAFARA RGDRDLAGIV SLRARPAAGD DTGDMRLLEG ADGPDAAREL VNCFRSIPNQ YPRSSGLMVF VS GPVTLAA MVGRAINPRI HGPVWWPYFR GGEYEPALEY PWPLISGPPR ILIATANAPE GENPTLDVEA ELKHLEEALA EPR KRKLCE VQRCPAATVS DITSALRSFK PHILHFIGHG TALGVYLRSA EHDGAQFVRG EDFQQMIATS LRQKDREMHL VVLN ACCTH ELAKALTEQV SCTIGTDIEV YDSASIHFAA RFYDHLVHGT SVHYAFNAAV DECRAHSTSG QEVFCLHPAA ERAPA SATP PVRADELVFF SP

UniProtKB: CHAT domain-containing protein

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Macromolecule #2: RNA (5'-R(*AP*AP*A)-3')

MacromoleculeName: RNA (5'-R(*AP*AP*A)-3') / type: rna / ID: 2 / Number of copies: 7
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 942.66 Da
SequenceString:
AAA

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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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38548
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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