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- EMDB-17416: Campylobacter jejuni flagellar motor, pflD deletion -

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Basic information

Entry
Database: EMDB / ID: EMD-17416
TitleCampylobacter jejuni flagellar motor, pflD deletion
Map dataCampylobacter jejuni pflD deletion bacterial flagellar motor
Sample
  • Organelle or cellular component: Campylobacter jejuni pflD deletion bacterial flagellar motor
Keywordsmolecular machine / bacterial flagellar motor / molecular evolution / in situ / MOTOR PROTEIN
Biological speciesCampylobacter jejuni (Campylobacter)
Methodsubtomogram averaging / cryo EM / Resolution: 58.0 Å
AuthorsDrobnic T / Henderson LD / Alzheimer M / Svensson S / Sharma CM / Beeby M
Funding support United Kingdom, United States, 6 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011178/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/V000799/1 United Kingdom
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI065539 United States
Cancer Research UKFC001143 United Kingdom
Wellcome TrustFC001143 United Kingdom
Medical Research Council (MRC, United Kingdom)FC001143 United Kingdom
CitationJournal: bioRxiv / Year: 2024
Title: Molecular model of a bacterial flagellar motor reveals a "parts-list" of protein adaptations to increase torque.
Authors: Tina Drobnič / Eli J Cohen / Tom Calcraft / Mona Alzheimer / Kathrin Froschauer / Sarah Svensson / William H Hoffmann / Nanki Singh / Sriram G Garg / Louie Henderson / Trishant R Umrekar / ...Authors: Tina Drobnič / Eli J Cohen / Tom Calcraft / Mona Alzheimer / Kathrin Froschauer / Sarah Svensson / William H Hoffmann / Nanki Singh / Sriram G Garg / Louie Henderson / Trishant R Umrekar / Andrea Nans / Deborah Ribardo / Francesco Pedaci / Ashley L Nord / Georg K A Hochberg / David R Hendrixson / Cynthia M Sharma / Peter B Rosenthal / Morgan Beeby /
Abstract: One hurdle to understanding how molecular machines work, and how they evolve, is our inability to see their structures . Here we describe a minicell system that enables cryogenic electron microscopy ...One hurdle to understanding how molecular machines work, and how they evolve, is our inability to see their structures . Here we describe a minicell system that enables cryogenic electron microscopy imaging and single particle analysis to investigate the structure of an iconic molecular machine, the bacterial flagellar motor, which spins a helical propeller for propulsion. We determine the structure of the high-torque motor including the subnanometre-resolution structure of the periplasmic scaffold, an adaptation essential to high torque. Our structure enables identification of new proteins, and interpretation with molecular models highlights origins of new components, reveals modifications of the conserved motor core, and explain how these structures both template a wider ring of motor proteins, and buttress the motor during swimming reversals. We also acquire insights into universal principles of flagellar torque generation. This approach is broadly applicable to other membrane-residing bacterial molecular machines complexes.
History
DepositionMay 22, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17416.png

Downloads & links

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Map

FileDownload / File: emd_17416.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCampylobacter jejuni pflD deletion bacterial flagellar motor
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
7 Å/pix.
x 200 pix.
= 1400.4 Å		7 Å/pix.
x 200 pix.
= 1400.4 Å		7 Å/pix.
x 200 pix.
= 1400.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 7.002 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.85
Minimum - Maximum-4.03212 - 4.0472326
Average (Standard dev.)0.051242556 (±0.70472795)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 1400.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17416_msk_1.map
Projections & Slices
AxesZYX

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Half map: Campylobacter jejuni pflD deletion half map

Fileemd_17416_half_map_1.map
AnnotationCampylobacter jejuni pflD deletion half map
Projections & Slices
AxesZYX

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Half map: Campylobacter jejuni pflD deletion half map

Fileemd_17416_half_map_2.map
AnnotationCampylobacter jejuni pflD deletion half map
Projections & Slices
AxesZYX

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Slices (1/2)
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Sample components

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Entire : Campylobacter jejuni pflD deletion bacterial flagellar motor

EntireName: Campylobacter jejuni pflD deletion bacterial flagellar motor
Components
  • Organelle or cellular component: Campylobacter jejuni pflD deletion bacterial flagellar motor

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Supramolecule #1: Campylobacter jejuni pflD deletion bacterial flagellar motor

SupramoleculeName: Campylobacter jejuni pflD deletion bacterial flagellar motor
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Campylobacter jejuni (Campylobacter) / Strain: 81-176

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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: 7.4 / Details: PBS
GridModel: Quantifoil R2/2
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV
DetailsCells were grown on MH agar, resuspended in PBS and concentrated to theoretical OD600 ~10

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 3.3 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.5 µm
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C17 (17 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 58.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 195
ExtractionNumber tomograms: 217 / Number images used: 195
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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