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- EMDB-48698: Cryo-EM structure of CRISPR-associated cA4 bound Cat1 Trigonal fi... -

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Basic information

Entry
Database: EMDB / ID: EMD-48698
TitleCryo-EM structure of CRISPR-associated cA4 bound Cat1 Trigonal filament assembly
Map dataCryo-EM map after non-uniform refinement in cryo-Sparc.
Sample
  • Complex: Antiviral protein Cat1 - Cyclic Tetra-Adenylate Complex
    • RNA: RNA (5'-R(P*AP*AP*AP*A)-3')
    • Protein or peptide: Cat1 (CRISPR-associated TIR 1)
KeywordsCRISPR / antiphage defense / adaptive immunity / Filament / CARF / TIR / cA4 / ANTIVIRAL PROTEIN
Biological speciesbacterium (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsMajumder P / Patel DJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)GM129430 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)GM145888 United States
CitationJournal: Science / Year: 2025
Title: Cat1 forms filament networks to degrade NAD during the type III CRISPR-Cas antiviral response
Authors: Baca CF / Majumder P / Hickling JH / Patel DJ / Marraffini LA
History
DepositionJan 17, 2025-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48698.png

Downloads & links

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Map

FileDownload / File: emd_48698.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map after non-uniform refinement in cryo-Sparc.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.154
Minimum - Maximum-0.28209415 - 0.80634844
Average (Standard dev.)0.005027631 (±0.03293709)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 373.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM half map B.

Fileemd_48698_half_map_1.map
AnnotationCryo-EM half map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half map A.

Fileemd_48698_half_map_2.map
AnnotationCryo-EM half map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Antiviral protein Cat1 - Cyclic Tetra-Adenylate Complex

EntireName: Antiviral protein Cat1 - Cyclic Tetra-Adenylate Complex
Components
  • Complex: Antiviral protein Cat1 - Cyclic Tetra-Adenylate Complex
    • RNA: RNA (5'-R(P*AP*AP*AP*A)-3')
    • Protein or peptide: Cat1 (CRISPR-associated TIR 1)

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Supramolecule #1: Antiviral protein Cat1 - Cyclic Tetra-Adenylate Complex

SupramoleculeName: Antiviral protein Cat1 - Cyclic Tetra-Adenylate Complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Cat1 protein forms filament structure upon recognition of cA4, Cyclic Tetra-Adenylate ligand.
Source (natural)Organism: bacterium (bacteria)

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Macromolecule #1: RNA (5'-R(P*AP*AP*AP*A)-3')

MacromoleculeName: RNA (5'-R(P*AP*AP*AP*A)-3') / type: rna / ID: 1 / Number of copies: 11
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.271866 KDa
SequenceString:
AAAA

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Macromolecule #2: Cat1 (CRISPR-associated TIR 1)

MacromoleculeName: Cat1 (CRISPR-associated TIR 1) / type: protein_or_peptide / ID: 2 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: bacterium (bacteria)
Molecular weightTheoretical: 30.150592 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPQAFFSHNN KDKKIVLEVL EHLRQSLVAT WIDQQSIPGG GSLIQQIIAG ISKSQYFLAF LSNEYLKSDW CWDELEQAYA LHQKGKVKI IPILLTNRAQ LDLNALTDAR RNFLESILTR LKYVEFDPHN MTRSLGSVAE ALWQNEAVRF EPIRMIKVNG T ELQVVEFK ...String:
MPQAFFSHNN KDKKIVLEVL EHLRQSLVAT WIDQQSIPGG GSLIQQIIAG ISKSQYFLAF LSNEYLKSDW CWDELEQAYA LHQKGKVKI IPILLTNRAQ LDLNALTDAR RNFLESILTR LKYVEFDPHN MTRSLGSVAE ALWQNEAVRF EPIRMIKVNG T ELQVVEFK IPGSNLPVDF LHHWDLKIED FIATSPNEQK PVKFDVPVAL YGPGPNWLYA FLTLPFKNRN TVFVFNSRTS EY ICVYSKS AGLAPGMVLK GHHHHH

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration1.2 mg/mL
BufferpH: 6
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: liquid-nitrogen-cooled liquid ethane was used as the cryogen..

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.03 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84493
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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