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- PDB-9n8m: In situ sheathed flagellar FlaC filament in Vibrio cholerae. -

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Basic information

Entry
Database: PDB / ID: 9n8m
TitleIn situ sheathed flagellar FlaC filament in Vibrio cholerae.
ComponentsFlagellin C
KeywordsMOTOR PROTEIN / In situ cryo-EM / sheathed flagellar filament / FlaC / 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 / single particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsWangbiao, G. / Rajeev, K.
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
M1: Flagellin C
M2: Flagellin C
M3: Flagellin C
M4: Flagellin C
M5: Flagellin C
M6: Flagellin C
M7: Flagellin C
M8: Flagellin C
M9: Flagellin C
MA: Flagellin C
MB: Flagellin C
MC: Flagellin C
MD: Flagellin C
ME: Flagellin C
MF: Flagellin C
MG: Flagellin C
MH: Flagellin C
MI: Flagellin C
MJ: Flagellin C
MK: Flagellin C
ML: Flagellin C
MM: Flagellin C
MN: Flagellin C
MO: Flagellin C
MP: Flagellin C
MQ: Flagellin C
MR: Flagellin C
MS: Flagellin C
MT: Flagellin C
MU: Flagellin C
MV: Flagellin C
MW: Flagellin C
MX: Flagellin C


Theoretical massNumber of molelcules
Total (without water)1,318,15633
Polymers1,318,15633
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 C


Mass: 39944.117 Da / Num. of mol.: 33 / Source method: isolated from a natural source
Source: (natural) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: P0C6C5
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Sheathed flagellar filament in DflhGDflaBDE Vibrio cholerae.
Type: COMPLEX
Details: In situ sheathed flagellar filament of DflhGDflaBDE Vibrio cholerae.
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
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

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 300613 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 138.79 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002792763
ELECTRON MICROSCOPYf_angle_d0.5591125169
ELECTRON MICROSCOPYf_chiral_restr0.037914784
ELECTRON MICROSCOPYf_plane_restr0.002116830
ELECTRON MICROSCOPYf_dihedral_angle_d5.005813175

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