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- EMDB-23623: Caulobacter crescentus expressing PopZ with IDR-156 -

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Basic information

Entry
Database: EMDB / ID: EMD-23623
TitleCaulobacter crescentus expressing PopZ with IDR-156
Map dataCaulobacter crescentus expressing PopZ with IDR-156
Sample
  • Cell: Caulobacter crescentus cells expressing PopZ with IDR-156
Biological speciesCaulobacter vibrioides NA1000 (bacteria)
Methodelectron tomography / cryo EM
AuthorsLasker K / Boeynaems S / Lam V / Scholl D / Stainton E / Briner A / Jacquemyn M / Daelemans D / Deniz A / Villa E ...Lasker K / Boeynaems S / Lam V / Scholl D / Stainton E / Briner A / Jacquemyn M / Daelemans D / Deniz A / Villa E / Holehouse AS / Gitler AD / Shapiro L
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM7240-40 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM123494-01 United States
National Science Foundation (NSF, United States)1920374 United States
Citation
Journal: Nat Commun / Year: 2022
Title: The material properties of a bacterial-derived biomolecular condensate tune biological function in natural and synthetic systems
Authors: Lasker K / Boeynaems S / Lam V / Scholl D / Stainton E / Briner A / Jacquemyn M / Daelemans D / Deniz A / Villa E / Holehouse AS / Gitler AD / Shapiro L
#1: Journal: biorxiv / Year: 2021
Title: A modular platform for engineering function of natural and synthetic biomolecular condensates
Authors: Lasker K / Boeynaems S / Lam V / Stainton E / Jacquemyn M / Daelemans D / Villa E / Holehouse AS / Gitler AD / Shapiro L
History
DepositionMar 15, 2021-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateOct 5, 2022-
Current statusOct 5, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_23623.png

Downloads & links

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Map

FileDownload / File: emd_23623.map.gz / Format: CCP4 / Size: 377.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCaulobacter crescentus expressing PopZ with IDR-156
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
17.06 Å/pix.
x 111 pix.
= 1893.66 Å		17.06 Å/pix.
x 928 pix.
= 15831.68 Å		17.06 Å/pix.
x 960 pix.
= 16377.6 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: 17.06 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-19.504175 - 15.703563
Average (Standard dev.)0.118015766 (±0.23792008)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin20-2351
Dimensions928960111
Spacing960928111
CellA: 16377.6 Å / B: 15831.68 Å / C: 1893.6599 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 cells expressing PopZ with IDR-156

EntireName: Caulobacter crescentus cells expressing PopZ with IDR-156
Components
  • Cell: Caulobacter crescentus cells expressing PopZ with IDR-156

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Supramolecule #1: Caulobacter crescentus cells expressing PopZ with IDR-156

SupramoleculeName: Caulobacter crescentus cells expressing PopZ with IDR-156
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Caulobacter vibrioides NA1000 (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: 7.4 / Details: M2 minimal media, supplemented with glucose.
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.019 kPa / Details: current 20 mA Instrument: PELCO easiGlow
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER
DetailsProtein expression was induced 4-5 hours prior to plunge freezing. Cells were concentrated to an OD600 ~3.0 by centrifugation.
Cryo protectantTrehalose
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.01 nA / Focused ion beam - Duration: 2700 sec. / Focused ion beam - Temperature: 77 K / Focused ion beam - Initial thickness: 500 nm / Focused ion beam - Final thickness: 150 nm
Focused ion beam - Details: milling current varies from 0.5 nA to 10 pA during milling.. The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Aquilos Cryo-FIB. This is not in a list ...Focused ion beam - Details: milling current varies from 0.5 nA to 10 pA during milling.. The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Aquilos Cryo-FIB. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 77.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-15 / Number real images: 47 / Average exposure time: 2.39 sec. / Average electron dose: 3.13 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus min: 5.0 µm / Nominal magnification: 33000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.10.29) / Number images used: 47

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