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- EMDB-53357: Cryo-electron tomograms of cryo-FIB milled E. coli lacking LpoB. -

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Basic information

Entry
Database: EMDB / ID: EMD-53357
TitleCryo-electron tomograms of cryo-FIB milled E. coli lacking LpoB.
Map dataDividing E.coli cell lacking LpoB. Septation stage.
Sample
  • Cell: Dividing E. coli cells lacking LpoB
KeywordsPBP1b / bacteria / division / peptidoglycan / CELL CYCLE
Biological speciesEscherichia coli (E. coli)
Methodelectron tomography / cryo EM
AuthorsNavarro PP / Bernhardt TG
Funding supportEuropean Union, Switzerland, United States, 5 items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF_89-2019European Union
Swiss National Science FoundationP500PB_203143 Switzerland
Swiss National Science FoundationTMSGI3_218251 Switzerland
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI083365 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM142553 United States
CitationJournal: Biorxiv / Year: 2025
Title: The aPBP-type cell wall synthase PBP1b plays a specialized role in fortifying the Escherichia coli division site against osmotic rupture
Authors: Navarro PP / Vettiger A / Hajdu R / Ananda VY / Lopez-Tavares A / Schmid EW / Walter JC / Loose M / Chao LH / Bernhardt TG
History
DepositionApr 9, 2025-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53357.png

Downloads & links

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Map

FileDownload / File: emd_53357.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationDividing E.coli cell lacking LpoB. Septation stage.
Voxel sizeX=Y=Z: 21.64 Å
Density
Minimum - Maximum-128.0 - 86.0
Average (Standard dev.)11.707952499999999 (±3.4287472)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-104104-44
Dimensions72051187
Spacing51172087
CellA: 11058.04 Å / B: 15580.8 Å / C: 1882.6799 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Dividing E.coli cell lacking LpoB. Septation stage. Low-passed.

Fileemd_53357_additional_1.map
AnnotationDividing E.coli cell lacking LpoB. Septation stage. Low-passed.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Dividing E.coli cell lacking LpoB. Cytokinesis stage.

Fileemd_53357_additional_10.map
AnnotationDividing E.coli cell lacking LpoB. Cytokinesis stage.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Dividing E.coli cell lacking LpoB. Constriction stage. Low-passed.

Fileemd_53357_additional_2.map
AnnotationDividing E.coli cell lacking LpoB. Constriction stage. Low-passed.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Dividing E.coli cell lacking LpoB. Constriction stage.

Fileemd_53357_additional_3.map
AnnotationDividing E.coli cell lacking LpoB. Constriction stage.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Dividing E.coli cell lacking LpoB. Constriction stage. Low-passed.

Fileemd_53357_additional_4.map
AnnotationDividing E.coli cell lacking LpoB. Constriction stage. Low-passed.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Dividing E.coli cell lacking LpoB. Septation stage.

Fileemd_53357_additional_5.map
AnnotationDividing E.coli cell lacking LpoB. Septation stage.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Dividing E.coli cell lacking LpoB. Septation stage. Low-passed.

Fileemd_53357_additional_6.map
AnnotationDividing E.coli cell lacking LpoB. Septation stage. Low-passed.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Dividing E.coli cell lacking LpoB. Constriction stage.

Fileemd_53357_additional_7.map
AnnotationDividing E.coli cell lacking LpoB. Constriction stage.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Pole of E.coli lacking LpoB.

Fileemd_53357_additional_8.map
AnnotationPole of E.coli lacking LpoB.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Dividing E.coli cell lacking LpoB. Septation stage.

Fileemd_53357_additional_9.map
AnnotationDividing E.coli cell lacking LpoB. Septation stage.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dividing E. coli cells lacking LpoB

EntireName: Dividing E. coli cells lacking LpoB
Components
  • Cell: Dividing E. coli cells lacking LpoB

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Supramolecule #1: Dividing E. coli cells lacking LpoB

SupramoleculeName: Dividing E. coli cells lacking LpoB / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K-12

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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: 7.5 / Details: LB media
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: glow discharged for 30 seconds at 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
Details: One-side blotting time of 13 seconds and blotting force of 10. Customized parafilm sheets were used for one-side blotting..
DetailsCells grown to O.D600 = 0.3.
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.1 / Focused ion beam - Duration: 1200 / Focused ion beam - Temperature: 83 K / Focused ion beam - Initial thickness: 1200 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos 2. 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

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 6 / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 7.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 33000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 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 reconstructionSoftware - Name: IMOD / Number images used: 40

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