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- PDB-9rcd: Sheathed flagellar filament in Vibrio alginolyticus -

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Basic information

Entry
Database: PDB / ID: 9rcd
TitleSheathed flagellar filament in Vibrio alginolyticus
ComponentsFlagellin
KeywordsSTRUCTURAL PROTEIN / FlaA / flagellin / filament / Vibrio alginolyticus
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsQin, K. / Einenkel, R. / Erhardt, M. / Bergeron, J.R.C.
Funding support United Kingdom, France, 2items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1May 6, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1May 6, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Flagellin
2: Flagellin
3: Flagellin
A: Flagellin
B: Flagellin
C: Flagellin
D: Flagellin
E: Flagellin
F: Flagellin
G: Flagellin
H: Flagellin
I: Flagellin
J: Flagellin
K: Flagellin
L: Flagellin
M: Flagellin
N: Flagellin
O: Flagellin
P: Flagellin
Q: Flagellin
R: Flagellin
S: Flagellin
T: Flagellin
U: Flagellin
V: Flagellin
c: Flagellin
h: Flagellin
i: Flagellin
j: Flagellin
k: Flagellin
l: Flagellin
m: Flagellin
n: Flagellin
o: Flagellin
p: Flagellin
q: Flagellin
r: Flagellin
s: Flagellin
t: Flagellin
u: Flagellin
v: Flagellin
w: Flagellin
x: Flagellin
z: Flagellin


Theoretical massNumber of molelcules
Total (without water)1,764,97844
Polymers1,764,97844
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Flagellin


Mass: 40113.129 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / References: UniProt: B9VXZ1
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Flagellar filament in Vibrio alginolyticus / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Source (natural)Organism: Vibrio alginolyticus (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA PLUNGER / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72779 / Symmetry type: POINT

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