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- EMDB-41046: Subtomogram average structure of the injectisome -

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Basic information

Entry
Database: EMDB / ID: EMD-41046
TitleSubtomogram average structure of the injectisome
Map data
Sample
  • Complex: Type 3 secretion systemType three secretion system
KeywordsT3SS / Salmonella / Injectisome / CELL INVASION
Biological speciesSalmonella enterica (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 25.0 Å
AuthorsPark D
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI152421 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI087946 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI114618 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI055472 United States
CitationJournal: Nat Microbiol / Year: 2023
Title: Parkinson's disease kinase LRRK2 coordinates a cell-intrinsic itaconate-dependent defence pathway against intracellular Salmonella.
Authors: Huan Lian / Donghyun Park / Meixin Chen / Florian Schueder / Maria Lara-Tejero / Jun Liu / Jorge E Galán /
Abstract: Cell-intrinsic defences constitute the first line of defence against intracellular pathogens. The guanosine triphosphatase RAB32 orchestrates one such defence response against the bacterial pathogen ...Cell-intrinsic defences constitute the first line of defence against intracellular pathogens. The guanosine triphosphatase RAB32 orchestrates one such defence response against the bacterial pathogen Salmonella, through delivery of antimicrobial itaconate. Here we show that the Parkinson's disease-associated leucine-rich repeat kinase 2 (LRRK2) orchestrates this defence response by scaffolding a complex between RAB32 and aconitate decarboxylase 1, which synthesizes itaconate from mitochondrial precursors. Itaconate delivery to Salmonella-containing vacuoles was impaired and Salmonella replication increased in LRRK2-deficient cells. Loss of LRRK2 also restored virulence of a Salmonella mutant defective in neutralizing this RAB32-dependent host defence pathway in mice. Cryo-electron tomography revealed tether formation between Salmonella-containing vacuoles and host mitochondria upon Salmonella infection, which was significantly impaired in LRRK2-deficient cells. This positions LRRK2 centrally within a host defence mechanism, which may have favoured selection of a common familial Parkinson's disease mutant allele in the human population.
History
DepositionJun 12, 2023-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateOct 11, 2023-
Current statusOct 11, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41046.png

Downloads & links

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Map

FileDownload / File: emd_41046.map.gz / Format: CCP4 / Size: 5.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 9.12 Å
Density
Contour LevelBy AUTHOR: 0.105
Minimum - Maximum-0.6872918 - 1.0329641
Average (Standard dev.)0.037063863 (±0.12357823)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100140
Spacing100100140
CellA: 912.0 Å / B: 912.0 Å / C: 1276.7999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41046_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_41046_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 : Type 3 secretion system

EntireName: Type 3 secretion systemType three secretion system
Components
  • Complex: Type 3 secretion systemType three secretion system

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Supramolecule #1: Type 3 secretion system

SupramoleculeName: Type 3 secretion system / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Salmonella enterica (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 43 / Number images used: 348
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 226

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