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- EMDB-47557: Representative tomogram of Caulobacter crescentus with WT-PopZ -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-47557
TitleRepresentative tomogram of Caulobacter crescentus with WT-PopZ
Map dataTomogram
Sample
  • Cell: Caulobacter crescentus expressing WT-polar organizing protein Z (PopZ)
Keywordsbacteria / condensate / phase separation / PROTEIN FIBRIL
Biological speciesCaulobacter vibrioides (bacteria)
Methodelectron tomography / cryo EM
AuthorsLasker K / Park D
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Seeing the forest and the trees: a multiscale depiction of PopZ condensation
Authors: Scholl D / Boyd T / Latham AP / Salazar A / Khan A / Boeynaems S / Holehouse AS / Lander GC / Sali A / Park D / Deniz AA / Lasker K
History
DepositionOct 29, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47557.png

Downloads & links

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Map

FileDownload / File: emd_47557.map.gz / Format: CCP4 / Size: 842.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.3 Å/pix.
x 600 pix.
= 7980. Å		13.3 Å/pix.
x 720 pix.
= 9576. Å		13.3 Å/pix.
x 511 pix.
= 6796.3 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 13.3 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-48.591206 - 8.362886
Average (Standard dev.)-0.4614543 (±0.3121386)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720511600
Spacing511720600
CellA: 6796.3003 Å / B: 9576.0 Å / C: 7980.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Caulobacter crescentus expressing WT-polar organizing protein Z (PopZ)

EntireName: Caulobacter crescentus expressing WT-polar organizing protein Z (PopZ)
Components
  • Cell: Caulobacter crescentus expressing WT-polar organizing protein Z (PopZ)

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Supramolecule #1: Caulobacter crescentus expressing WT-polar organizing protein Z (PopZ)

SupramoleculeName: Caulobacter crescentus expressing WT-polar organizing protein Z (PopZ)
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Caulobacter vibrioides (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 2 / Focused ion beam - Current: 10 / Focused ion beam - Duration: 600 / Focused ion beam - Temperature: 83 K / Focused ion beam - Initial thickness: 20000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos II. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 35
CTF correctionType: NONE

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