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- EMDB-16724: Periplasmic scaffold of the Campylobacter jejuni flagellar motor -

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Basic information

Entry
Database: EMDB / ID: EMD-16724
TitlePeriplasmic scaffold of the Campylobacter jejuni flagellar motor
Map dataPeriplasmic scaffold of the Campylobacter jejuni flagellar motor, LAFTER-filtered map
Sample
  • Organelle or cellular component: Periplasmic scaffold structures of the Campylobacter jejuni flagellar motor
    • Complex: Basal disk (part)
    • Complex: Periplasmic scaffold
Keywordsmolecular machines / bacterial flagellar motor / molecular evolution / in situ / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / chemotaxis / membrane / plasma membrane
Similarity search - Function
Flagellar protein FlgP / FlgT, N-terminal domain superfamily / Flagellar basal body-associated protein FliL / Flagellar basal body-associated protein FliL / Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / PDZ domain / PDZ domain 6 / : / OmpA-like domain profile. ...Flagellar protein FlgP / FlgT, N-terminal domain superfamily / Flagellar basal body-associated protein FliL / Flagellar basal body-associated protein FliL / Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / PDZ domain / PDZ domain 6 / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / PDZ domain / OmpA-like domain / Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Paralyzed flagella protein PflA / Chemotaxis protein MotB, putative / Lipoprotein, putative / Flagellar protein FliL / TPR domain protein / PDZ domain-containing protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsDrobnic T / Cohen EJ / Singh NK / Umrekar TR / Nans A / Rosenthal PB / Beeby M
Funding support United Kingdom, France, United States, 7 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
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI065539 United States
Cancer Research UKFC001143 United Kingdom
Medical Research Council (MRC, United Kingdom)FC001143 United Kingdom
Wellcome TrustFC001143 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
DepositionFeb 19, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16724.png

Downloads & links

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Map

FileDownload / File: emd_16724.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPeriplasmic scaffold of the Campylobacter jejuni flagellar motor, LAFTER-filtered map
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: 0.19
Minimum - Maximum-0.9982731 - 1.1889858
Average (Standard dev.)-0.00001924071 (±0.013055228)
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: Periplasmic scaffold of the Campylobacter jejuni flagellar motor,...

Fileemd_16724_additional_1.map
AnnotationPeriplasmic scaffold of the Campylobacter jejuni flagellar motor, RELION 3D-refine map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map of the periplasmic scaffold of the Campylobacter...

Fileemd_16724_half_map_1.map
AnnotationHalf-map of the periplasmic scaffold of the Campylobacter jejuni flagellar motor
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map of the periplasmic scaffold of the Campylobacter...

Fileemd_16724_half_map_2.map
AnnotationHalf-map of the periplasmic scaffold of the Campylobacter jejuni flagellar motor
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Periplasmic scaffold structures of the Campylobacter jejuni flage...

EntireName: Periplasmic scaffold structures of the Campylobacter jejuni flagellar motor
Components
  • Organelle or cellular component: Periplasmic scaffold structures of the Campylobacter jejuni flagellar motor
    • Complex: Basal disk (part)
    • Complex: Periplasmic scaffold

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Supramolecule #1: Periplasmic scaffold structures of the Campylobacter jejuni flage...

SupramoleculeName: Periplasmic scaffold structures of the Campylobacter jejuni flagellar motor
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Campylobacter jejuni (Campylobacter) / Strain: 81-176

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Supramolecule #2: Basal disk (part)

SupramoleculeName: Basal disk (part) / type: complex / ID: 2 / Parent: 1
Details: Innermost ring of the basal disk, made of protein FlgP
Source (natural)Organism: Campylobacter jejuni (Campylobacter) / Strain: 81-176

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Supramolecule #3: Periplasmic scaffold

SupramoleculeName: Periplasmic scaffold / type: complex / ID: 3 / Parent: 1
Details: A protein scaffold in the C. jejuni motor incorporates stator complexes for flagellar motility
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
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C17 (17 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.9 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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