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- EMDB-53917: Sheathed flagellar filament in Vibrio alginolyticus -

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Basic information

Entry
Database: EMDB / ID: EMD-53917
TitleSheathed flagellar filament in Vibrio alginolyticus
Map dataSheathed filament in Vibrio alginolyticus
Sample
  • Organelle or cellular component: Flagellar filament in Vibrio alginolyticus
    • Protein or peptide: Flagellin
KeywordsFlaA / flagellin / filament / Vibrio alginolyticus / STRUCTURAL PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
Flagellin hook, IN motif / Flagellin hook IN motif / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Biological speciesVibrio alginolyticus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsQin K / Einenkel R / Erhardt M / Bergeron JRC
Funding support United Kingdom, France, 2 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R009759/2 United Kingdom
Human Frontier Science Program (HFSP)RGY0080/2021 France
CitationJournal: Nat Commun / Year: 2026
Title: The structure of the Vibrio alginolyticus flagellar filament suggests molecular mechanism for the rotation of sheathed flagella.
Authors: Kailin Qin / Rosa Einenkel / Weilong Zhao / Caroline Kühne / Joseph Atherton / Marc Erhardt / Julien R C Bergeron /
Abstract: In several pathogenic bacteria, including Vibrio species, the filament of the bacterial flagellum is encased by a membranous sheath, an extension of the bacterial outer membrane. It has been proposed ...In several pathogenic bacteria, including Vibrio species, the filament of the bacterial flagellum is encased by a membranous sheath, an extension of the bacterial outer membrane. It has been proposed that having sheathed flagella permit bacteria to evade an immune response against flagellar components, suggesting a role in virulence. However, the molecular details of the interaction between sheath and filament, and how it impacts filament rotation, remain largely uncharacterized. Here, we combine single-particle cryo-electron microscopy, cryo-electron tomography, and genetic analyses to resolve the molecular architecture and biogenesis of the sheathed flagellum in Vibrio alginolyticus. We show that the flagellar filament forms a canonical 11-stranded supercoil made of the flagellin FlaD2 and enveloped by a bilayered sheath. We report that the filament surface is highly electronegative, suggesting that electrostatic repulsion between filament and sheath may reduce friction and supports high-speed flagellar rotation. We also show that the filament cap protein FliD possesses a unique domain in sheathed flagella, that may coordinate sheath assembly with filament elongation. Collectively, this structural insight into the structure of the Vibrio alginolyticus flagellum suggests a molecular mechanism for the rotation of sheathed flagella.
History
DepositionMay 27, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53917.png

Downloads & links

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Map

FileDownload / File: emd_53917.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSheathed filament in Vibrio alginolyticus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 500 pix.
= 550. Å		1.1 Å/pix.
x 500 pix.
= 550. Å		1.1 Å/pix.
x 500 pix.
= 550. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.3920453 - 0.5636767
Average (Standard dev.)0.0056158644 (±0.03787948)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 550.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_53917_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_53917_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Flagellar filament in Vibrio alginolyticus

EntireName: Flagellar filament in Vibrio alginolyticus
Components
  • Organelle or cellular component: Flagellar filament in Vibrio alginolyticus
    • Protein or peptide: Flagellin

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Supramolecule #1: Flagellar filament in Vibrio alginolyticus

SupramoleculeName: Flagellar filament in Vibrio alginolyticus / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio alginolyticus (bacteria)

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 44 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria)
Molecular weightTheoretical: 40.113129 KDa
SequenceString: MAVNVNTNVS AMTAQRYLNN ANSAQQTSME RLSSGFKINS AKDDAAGLQI SNRLNVQSRG LDVAVRNAND GISIAQTAEG AMNETTNIL QRMRDLSLQS ANGSNSKAER VAIQEEVTAL NDELNRIAET TSFGGNKLLN GTHGAKSFQI GADNGEAVML E LKDMRSDN ...String:
MAVNVNTNVS AMTAQRYLNN ANSAQQTSME RLSSGFKINS AKDDAAGLQI SNRLNVQSRG LDVAVRNAND GISIAQTAEG AMNETTNIL QRMRDLSLQS ANGSNSKAER VAIQEEVTAL NDELNRIAET TSFGGNKLLN GTHGAKSFQI GADNGEAVML E LKDMRSDN KMMGGVSYQA ESGKGKDWNV AEGKNDLKIN LTDSYGQEQE INISAKAGDD IEELATYING QTDLVKASVD QD GKLQIFA GNNKVEGEVE FSGGLSGELG LGEGKKVTVD TIDVTSVGGA QESVAIIDAA LKYVDSHRAE LGAFQNRFNH AIS NLDNIN ENVNASKSRI KDTDFAKETT AMTKSQILSQ ASSSILAQAK QAPNSALSLL G

UniProtKB: Flagellin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: LEICA PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72779
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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