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- EMDB-16174: Saccharolobus solfataricus type III-D CRISPR effector - Body 1 -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-16174
TitleSaccharolobus solfataricus type III-D CRISPR effector - Body 1
Map dataMap Body 1
Sample
  • Complex: Body 1 - Saccharolobus solfataricus type III-D CRISPR effector
KeywordsSulfolobus / CRISPR / Type III-D / ANTIVIRAL PROTEIN
Biological speciesSaccharolobus solfataricus (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSpagnolo L / White MF
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Curr Res Struct Biol / Year: 2023
Title: Structure of the type III-D CRISPR effector.
Authors: Giuseppe Cannone / Dmytro Kompaniiets / Shirley Graham / Malcolm F White / Laura Spagnolo /
Abstract: CRISPR-Cas is a prokaryotic adaptive immune system, classified into six different types, each characterised by a signature protein. Type III systems, classified based on the presence of a Cas10 ...CRISPR-Cas is a prokaryotic adaptive immune system, classified into six different types, each characterised by a signature protein. Type III systems, classified based on the presence of a Cas10 subunit, are rather diverse multi-subunit assemblies with a range of enzymatic activities and downstream ancillary effectors. The broad array of current biotechnological CRISPR applications is mainly based on proteins classified as Type II, however recent developments established the feasibility and efficacy of multi-protein Type III CRISPR-Cas effector complexes as RNA-targeting tools in eukaryotes. The crenarchaeon has two type III system subtypes (III-B and III-D). Here, we report the cryo-EM structure of the Csm Type III-D complex from (SsoCsm), which uses CRISPR RNA to bind target RNA molecules, activating the Cas10 subunit for antiviral defence. The structure reveals the complex organisation, subunit/subunit connectivity and protein/guide RNA interactions of the SsoCsm complex, one of the largest CRISPR effectors known.
History
DepositionNov 19, 2022-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16174.png

Downloads & links

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Map

FileDownload / File: emd_16174.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap Body 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 300 pix.
= 313.8 Å		1.05 Å/pix.
x 300 pix.
= 313.8 Å		1.05 Å/pix.
x 300 pix.
= 313.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.046 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0085
Minimum - Maximum-0.020727929 - 0.04285446
Average (Standard dev.)-0.00032371856 (±0.0011473198)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 313.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map Body 1

Fileemd_16174_half_map_1.map
AnnotationHalf map Body 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map Body 1

Fileemd_16174_half_map_2.map
AnnotationHalf map Body 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Body 1 - Saccharolobus solfataricus type III-D CRISPR effector

EntireName: Body 1 - Saccharolobus solfataricus type III-D CRISPR effector
Components
  • Complex: Body 1 - Saccharolobus solfataricus type III-D CRISPR effector

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Supramolecule #1: Body 1 - Saccharolobus solfataricus type III-D CRISPR effector

SupramoleculeName: Body 1 - Saccharolobus solfataricus type III-D CRISPR effector
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharolobus solfataricus (archaea)

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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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 0.0 µm / Nominal defocus min: 0.0 µm
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 34.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 192787

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