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- EMDB-27111: Intracellular Coxiella 6hpi -

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Basic information

Entry
Database: EMDB / ID: EMD-27111
TitleIntracellular Coxiella 6hpi
Map data
Sample
  • Cell: COS-7 cell infected with Coxiella 6hpi
Biological speciesCoxiella burnetii (bacteria)
Methodelectron tomography / cryo EM
AuthorsPark D / Liu J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI152421-02 United States
CitationJournal: Infect Immun / Year: 2022
Title: Developmental Transitions Coordinate Assembly of the Coxiella burnetii Dot/Icm Type IV Secretion System.
Authors: Donghyun Park / Samuel Steiner / Meng Shao / Craig R Roy / Jun Liu /
Abstract: Coxiella burnetii is an obligate intracellular bacterial pathogen that has evolved a unique biphasic developmental cycle. The infectious form of C. burnetii is the dormant small cell variant (SCV), ...Coxiella burnetii is an obligate intracellular bacterial pathogen that has evolved a unique biphasic developmental cycle. The infectious form of C. burnetii is the dormant small cell variant (SCV), which transitions to a metabolically active large cell variant (LCV) that replicates inside the lysosome-derived host vacuole. A Dot/Icm type IV secretion system (T4SS), which can deliver over 100 effector proteins to host cells, is essential for the biogenesis of the vacuole and intracellular replication. How the distinct C. burnetii life cycle impacts the assembly and function of the Dot/Icm T4SS has remained unknown. Here, we combine advanced cryo-focused ion beam (cryo-FIB) milling and cryo-electron tomography (cryo-ET) imaging to visualize all developmental transitions and the assembly of the Dot/Icm T4SS . Importantly, assembled Dot/Icm machines were not present in the infectious SCV. The appearance of the assembled Dot/Icm machine correlated with the transition of the SCV to the LCV intracellularly. Furthermore, temporal characterization of C. burnetii morphological changes revealed regions of the inner membrane that invaginate to form tightly packed stacks during the LCV-to-SCV transition at late stages of infection, which may enable the SCV-to-LCV transition that occurs upon infection of a new host cell. Overall, these data establish how C. burnetii developmental transitions control critical bacterial processes to promote intracellular replication and transmission.
History
DepositionMay 26, 2022-
Header (metadata) releaseOct 19, 2022-
Map releaseOct 19, 2022-
UpdateNov 2, 2022-
Current statusNov 2, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27111.png

Downloads & links

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Map

FileDownload / File: emd_27111.map.gz / Format: CCP4 / Size: 1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
18.22 Å/pix.
x 132 pix.
= 2405.04 Å		18.22 Å/pix.
x 1440 pix.
= 26236.799 Å		18.22 Å/pix.
x 1440 pix.
= 26236.799 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: 18.22 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-4.7991824 - 4.7216887
Average (Standard dev.)2.6302105e-10 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin0-2080
Dimensions14401440132
Spacing14401440132
CellA: 26236.799 Å / B: 26236.799 Å / C: 2405.0398 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : COS-7 cell infected with Coxiella 6hpi

EntireName: COS-7 cell infected with Coxiella 6hpi
Components
  • Cell: COS-7 cell infected with Coxiella 6hpi

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Supramolecule #1: COS-7 cell infected with Coxiella 6hpi

SupramoleculeName: COS-7 cell infected with Coxiella 6hpi / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Coxiella burnetii (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
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 3 kV / Focused ion beam - Current: 0.05 nA / Focused ion beam - Duration: 3600 sec. / Focused ion beam - Temperature: 103 K / Focused ion beam - Initial thickness: 10000 nm / Focused ion beam - Final thickness: 150 nm
Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Aquilos. 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
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 33

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