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- EMDB-27105: Coxiella T4SS OMC -

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Basic information

Entry
Database: EMDB / ID: EMD-27105
TitleCoxiella T4SS OMC
Map dataFocused refined structure of Coxiella T4SS OMC
Sample
  • Complex: Outer membrane complex of Coxiella T4SS
KeywordsT4SS / Dot/Icm / secretion system / TRANSPORT PROTEIN
Biological speciesCoxiella burnetii (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 11.0 Å
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-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27105.png

Downloads & links

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Map

FileDownload / File: emd_27105.map.gz / Format: CCP4 / Size: 3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refined structure of Coxiella T4SS OMC
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.75 Å/pix.
x 92 pix.
= 252.724 Å		2.75 Å/pix.
x 92 pix.
= 252.724 Å		2.75 Å/pix.
x 92 pix.
= 252.724 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.747 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.126
Minimum - Maximum-0.56601346 - 1.13187
Average (Standard dev.)0.0040816567 (±0.060807366)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions929292
Spacing929292
CellA=B=C: 252.724 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_27105_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_27105_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Outer membrane complex of Coxiella T4SS

EntireName: Outer membrane complex of Coxiella T4SS
Components
  • Complex: Outer membrane complex of Coxiella T4SS

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Supramolecule #1: Outer membrane complex of Coxiella T4SS

SupramoleculeName: Outer membrane complex of Coxiella T4SS / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Coxiella burnetii (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: OTHER / Number subtomograms used: 7905
ExtractionNumber tomograms: 713 / Number images used: 7905
Final angle assignmentType: OTHER

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