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- EMDB-16723: Wild-type Campylobacter jejuni flagellar motor, in situ -

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Basic information

Entry
Database: EMDB / ID: EMD-16723
TitleWild-type Campylobacter jejuni flagellar motor, in situ
Map dataWT flagellar motor of Campylobacter jejuni, in situ
Sample
  • Complex: Wild-type flagellar motor of Campylobacter jejuni, in situ
Keywordsmolecular machine / bacterial flagellar motor / molecular evolution / in situ / MOTOR PROTEIN
Biological speciesCampylobacter jejuni (Campylobacter)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.36 Å
AuthorsDrobnic T / Cohen EJ / Calcraft T / Singh NK / Nans A / Rosenthal PB / Beeby M
Funding support United Kingdom, France, 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
Human Frontier Science Program (HFSP)RGP0028/2021-HOCHBERG France
Cancer Research UKFC001143 United Kingdom
Wellcome TrustFC001143 United Kingdom
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI065539 United States
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
DepositionFeb 19, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16723.png

Downloads & links

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Map

FileDownload / File: emd_16723.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationWT flagellar motor of Campylobacter jejuni, in situ
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 800 pix.
= 1760. Å		2.2 Å/pix.
x 800 pix.
= 1760. Å		2.2 Å/pix.
x 800 pix.
= 1760. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0012
Minimum - Maximum-0.019415455 - 0.018564876
Average (Standard dev.)0.00002019473 (±0.0006163044)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 1760.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Lathed map of the C. jejuni flagellar LP-rings

Fileemd_16723_additional_1.map
AnnotationLathed map of the C. jejuni flagellar LP-rings
Projections & Slices
AxesZYX

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Additional map: Lathed map of the C. jejuni flagellar MS-ring

Fileemd_16723_additional_2.map
AnnotationLathed map of the C. jejuni flagellar MS-ring
Projections & Slices
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Additional map: Lathed map of the C. jejuni flagellar C-ring

Fileemd_16723_additional_3.map
AnnotationLathed map of the C. jejuni flagellar C-ring
Projections & Slices
AxesZYX

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Histogram

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Half map: Campylobacter jejuni flagellar motor half map

Fileemd_16723_half_map_1.map
AnnotationCampylobacter jejuni flagellar motor half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Campylobacter jejuni flagellar motor half map

Fileemd_16723_half_map_2.map
AnnotationCampylobacter jejuni flagellar motor half 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 : Wild-type flagellar motor of Campylobacter jejuni, in situ

EntireName: Wild-type flagellar motor of Campylobacter jejuni, in situ
Components
  • Complex: Wild-type flagellar motor of Campylobacter jejuni, in situ

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Supramolecule #1: Wild-type flagellar motor of Campylobacter jejuni, in situ

SupramoleculeName: Wild-type flagellar motor of Campylobacter jejuni, in situ
type: complex / 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
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: PBS
GridModel: Quantifoil R0.6/1 / Material: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV
DetailsMinicells purified by centrifugation and concentrated to theoretical OD600 ~10

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Average exposure time: 17.0 sec. / #0 - Average electron dose: 50.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON III (4k x 4k) / #1 - Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
CTF correctionSoftware: (Name: CTFFIND (ver. 4.1.14), RELION (ver. 3.1.1))
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C17 (17 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 9.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 32790
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1) / Details: RELION SGD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1.1)
FSC plot (resolution estimation)

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