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- EMDB-38807: ICP1 Csy-dsDNA-Cas1-Cas2/3 complex (fully assembled form) with C2... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-38807
TitleICP1 Csy-dsDNA-Cas1-Cas2/3 complex (fully assembled form) with C2 symmetry
Map data
Sample
  • Complex: csy complex
KeywordsIMMUNE SYSTEM-RNA-DNA complex / RNA BINDING PROTEIN/DNA/RNA / RNA BINDING PROTEIN-DNA-RNA complex / ANTIBIOTIC
Biological speciesVibrio phage ICP1_2004_A (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsZhang LX / Feng Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32171274 China
CitationJournal: To Be Published
Title: ICP1 Csy-dsDNA-Cas1-Cas2/3 complex (fully assembled form) with C2 symmetry
Authors: Zhang LX / Feng Y
History
DepositionJan 22, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38807.png

Downloads & links

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Map

FileDownload / File: emd_38807.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.8519036 - 2.0330167
Average (Standard dev.)0.004426826 (±0.06961504)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38807_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_38807_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 : csy complex

EntireName: csy complex
Components
  • Complex: csy complex

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Supramolecule #1: csy complex

SupramoleculeName: csy complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 132865
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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