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- PDB-9x3v: Cryo-EM structure of the flagellar filament in Vibrio Cholerae -

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Basic information

Entry
Database: PDB / ID: 9x3v
TitleCryo-EM structure of the flagellar filament in Vibrio Cholerae
ComponentsFlagellin
KeywordsMOTOR PROTEIN / Flagella / Vibrio Cholerae / Filament / FlaA / Locomotion
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 cholerae (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsNg, C.H.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)T11-104/22-R Hong Kong
CitationJournal: To Be Published
Title: High resolution structures of flagella from Vibrio Cholerae and Vibrio parahaemolyticus: Insights into the basis of swimming and swarming
Authors: Liu, X.B. / Zhang, Y.Y. / Ng, C.H. / Wang, Z.L. / Leung, K.P. / Li, S.R. / Zheng, S.Q. / Heng, H. / Cheng, Q.P. / Xu, Y.T. / Chen, K.C. / Xie, M.M. / Sun, R.Y. / Luo, M. / Lau, C.Y. / Chen, S.
History
DepositionOct 9, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: 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)630,75616
Polymers630,75616
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Flagellin


Mass: 39422.238 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Vibrio cholerae (bacteria) / References: UniProt: A0A085S3I0
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of the flagellar filament in Vibrio Cholerae
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Vibrio cholerae (bacteria)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
250 mMSodium ChlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 65.4 ° / Axial rise/subunit: 4.73 Å / Axial symmetry: C1
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65443 / Symmetry type: HELICAL

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