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- PDB-9n8b: In situ unsheathed flagellar filament of Vibrio cholerae resolved... -

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Basic information

Entry
Database: PDB / ID: 9n8b
TitleIn situ unsheathed flagellar filament of Vibrio cholerae resolved with helical reconstruction.
ComponentsFlagellin D
KeywordsMOTOR PROTEIN / In situ cryo-EM / unsheathed flagellar filament / FlaD Vibrio cholerae.
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 O1 biovar El Tor str. N16961 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsWangbiao, G. / Jun, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI087946 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI132818 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of the sheathed flagellum in intact Vibrio cholerae
Authors: Wangbiao, G. / Sarah, Z. / Jian, Y. / Jin, H.P. / Venus, S. / Shenping, W. / Karl, E.K. / Fitnat, Y. / Jun, L.
History
DepositionFeb 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellin D
B: Flagellin D
C: Flagellin D
D: Flagellin D
E: Flagellin D
F: Flagellin D
G: Flagellin D
H: Flagellin D
I: Flagellin D
J: Flagellin D
K: Flagellin D
L: Flagellin D
M: Flagellin D
N: Flagellin D
O: Flagellin D
P: Flagellin D
Q: Flagellin D
R: Flagellin D
S: Flagellin D
T: Flagellin D
U: Flagellin D
V: Flagellin D
W: Flagellin D
X: Flagellin D
Y: Flagellin D
Z: Flagellin D
a: Flagellin D
b: Flagellin D
c: Flagellin D
d: Flagellin D
e: Flagellin D
f: Flagellin D
g: Flagellin D


Theoretical massNumber of molelcules
Total (without water)1,313,69133
Polymers1,313,69133
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Flagellin D


Mass: 39808.809 Da / Num. of mol.: 33
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: flaD, VC_2143
Production host: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: P0C6C6
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Vibrio cholerae serotype O1 / Type: CELL / Entity ID: all / Source: NATURAL
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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: 2200 nm / Nominal defocus min: 1600 nm
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 65.41 ° / Axial rise/subunit: 4.74 Å / Axial symmetry: C1
3D reconstructionResolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103479 / Symmetry type: HELICAL

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