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- PDB-9ydx: RBM3 domain of FliF protein in MS-ring of flagellar motor in Vibr... -

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Basic information

Entry
Database: PDB / ID: 9ydx
TitleRBM3 domain of FliF protein in MS-ring of flagellar motor in Vibrio cholerae
ComponentsFlagellar M-ring protein
KeywordsMOTOR PROTEIN / In situ cryo-EM / sheathed flagellar motor / Vibrio cholerae / MS-ring / FliF / assembled state
Function / homology
Function and homology information


bacterial-type flagellum basal body, MS ring / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / plasma membrane
Similarity search - Function
Flagellar M-ring protein FliF / Flagellar M-ring C-terminal / Flagellar M-ring protein C-terminal / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Flagellar M-ring protein
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsGuo, W. / Yue, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI087946 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI132818 United States
CitationJournal: To Be Published
Title: In-situ cryo-EM structures reveal mechanisms of sheathed flagellar assembly, rotation, and disassembly in Vibrio cholerae
Authors: Wangbiao, G. / Jian, Y. / Jin, H.P. / Fitnat, Y. / Jun, L.
History
DepositionSep 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data 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
Aa: Flagellar M-ring protein
Ab: Flagellar M-ring protein
Ac: Flagellar M-ring protein
Ad: Flagellar M-ring protein
Ae: Flagellar M-ring protein
Af: Flagellar M-ring protein
Ag: Flagellar M-ring protein
Ah: Flagellar M-ring protein
Ai: Flagellar M-ring protein
Aj: Flagellar M-ring protein
Ak: Flagellar M-ring protein
Al: Flagellar M-ring protein
Am: Flagellar M-ring protein
An: Flagellar M-ring protein
Ao: Flagellar M-ring protein
Ap: Flagellar M-ring protein
Aq: Flagellar M-ring protein
Ar: Flagellar M-ring protein
As: Flagellar M-ring protein
At: Flagellar M-ring protein
Au: Flagellar M-ring protein
Av: Flagellar M-ring protein
Aw: Flagellar M-ring protein
Ax: Flagellar M-ring protein
Ay: Flagellar M-ring protein
Az: Flagellar M-ring protein
Ba: Flagellar M-ring protein
Bb: Flagellar M-ring protein
Bc: Flagellar M-ring protein
Bd: Flagellar M-ring protein
Be: Flagellar M-ring protein
Bf: Flagellar M-ring protein
Bg: Flagellar M-ring protein
Bh: Flagellar M-ring protein


Theoretical massNumber of molelcules
Total (without water)730,85734
Polymers730,85734
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 ...
Flagellar M-ring protein / FliF


Mass: 21495.785 Da / Num. of mol.: 34 / Source method: isolated from a natural source
Source: (natural) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: Q9KQ69
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: Vibrio cholerae / 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: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
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
1Topazparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C34 (34 fold cyclic)
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44428 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 63.18 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003238930
ELECTRON MICROSCOPYf_angle_d0.535152564
ELECTRON MICROSCOPYf_chiral_restr0.04066188
ELECTRON MICROSCOPYf_plane_restr0.00346902
ELECTRON MICROSCOPYf_dihedral_angle_d13.216414790

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