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- EMDB-27106: Coxiella Small Cell Variant (SCV) -

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Basic information

Entry
Database: EMDB / ID: EMD-27106
TitleCoxiella Small Cell Variant (SCV)
Map dataRepresentative tomogram of Coxiella small cell variant (SCV)
Sample
  • Cell: Coxiella burnetii Small Cell Variant
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) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateNov 2, 2022-
Current statusNov 2, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27106.png

Downloads & links

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Map

FileDownload / File: emd_27106.map.gz / Format: CCP4 / Size: 798 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRepresentative tomogram of Coxiella small cell variant (SCV)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.99 Å/pix.
x 227 pix.
= 2494.73 Å		10.99 Å/pix.
x 960 pix.
= 10550.399 Å		10.99 Å/pix.
x 960 pix.
= 10550.399 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: 10.99 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-33.363373 - 14.747218
Average (Standard dev.)0.00021002762 (±1.0190612)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-17-1-8
Dimensions960960227
Spacing960960227
CellA: 10550.399 Å / B: 10550.399 Å / C: 2494.73 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Coxiella burnetii Small Cell Variant

EntireName: Coxiella burnetii Small Cell Variant
Components
  • Cell: Coxiella burnetii Small Cell Variant

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Supramolecule #1: Coxiella burnetii Small Cell Variant

SupramoleculeName: Coxiella burnetii Small Cell Variant / 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
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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: 35

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