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- PDB-9yee: Rod-hook protein in Vibrio cholerae at assembled, opened state -

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Basic information

Entry
Database: PDB / ID: 9yee
TitleRod-hook protein in Vibrio cholerae at assembled, opened state
Components
  • Flagellar basal-body rod protein FlgF
  • Flagellar basal-body rod protein FlgG
  • Flagellar hook protein FlgE
KeywordsMOTOR PROTEIN / In situ cryo-EM / sheathed flagellar motor / Vibrio cholerae / rod-hook / assembled state
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum hook / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / cytosol
Similarity search - Function
Flagellar basal-body rod FlgF / Flagellar basal-body rod FlgG / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, conserved site ...Flagellar basal-body rod FlgF / Flagellar basal-body rod FlgG / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagellar basal-body/hook protein, C-terminal domain / Flagella basal body rod protein / Flagellar basal body rod FlgEFG protein C-terminal
Similarity search - Domain/homology
Flagellar hook protein FlgE / Flagellar basal-body rod protein FlgF / Flagellar basal-body rod protein FlgG
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.44 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 24, 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: Additional map / Part number: 1 / Data content type: Additional map / 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
Ba: Flagellar basal-body rod protein FlgG
Bb: Flagellar basal-body rod protein FlgG
Bc: Flagellar basal-body rod protein FlgG
Bd: Flagellar basal-body rod protein FlgG
Be: Flagellar basal-body rod protein FlgG
Bf: Flagellar basal-body rod protein FlgG
Bg: Flagellar basal-body rod protein FlgG
Bh: Flagellar basal-body rod protein FlgG
Bi: Flagellar basal-body rod protein FlgG
Bj: Flagellar basal-body rod protein FlgG
Bk: Flagellar basal-body rod protein FlgG
Bl: Flagellar basal-body rod protein FlgG
Bm: Flagellar basal-body rod protein FlgG
Bn: Flagellar basal-body rod protein FlgG
Bo: Flagellar basal-body rod protein FlgG
Bp: Flagellar basal-body rod protein FlgG
Bq: Flagellar basal-body rod protein FlgG
Br: Flagellar basal-body rod protein FlgG
Bs: Flagellar basal-body rod protein FlgG
Bt: Flagellar basal-body rod protein FlgG
Bu: Flagellar basal-body rod protein FlgG
Bv: Flagellar basal-body rod protein FlgG
Bw: Flagellar basal-body rod protein FlgG
Bx: Flagellar basal-body rod protein FlgG
By: Flagellar basal-body rod protein FlgG
Bz: Flagellar basal-body rod protein FlgG
Ca: Flagellar basal-body rod protein FlgF
Cb: Flagellar basal-body rod protein FlgG
Cc: Flagellar basal-body rod protein FlgF
Cd: Flagellar basal-body rod protein FlgF
Ce: Flagellar hook protein FlgE
Cf: Flagellar hook protein FlgE
Cg: Flagellar hook protein FlgE
Ch: Flagellar hook protein FlgE
Ci: Flagellar hook protein FlgE
Cj: Flagellar hook protein FlgE
Ck: Flagellar hook protein FlgE
Cl: Flagellar hook protein FlgE
Cm: Flagellar hook protein FlgE
Cn: Flagellar hook protein FlgE
Co: Flagellar hook protein FlgE
Cp: Flagellar hook protein FlgE
Cq: Flagellar hook protein FlgE
Cr: Flagellar hook protein FlgE
Cs: Flagellar hook protein FlgE
Ct: Flagellar hook protein FlgE
Cu: Flagellar hook protein FlgE
Cv: Flagellar basal-body rod protein FlgF
Cw: Flagellar basal-body rod protein FlgF


Theoretical massNumber of molelcules
Total (without water)1,689,94449
Polymers1,689,94449
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 ...
Flagellar basal-body rod protein FlgG / Distal rod protein


Mass: 28114.350 Da / Num. of mol.: 27 / Source method: isolated from a natural source
Source: (natural) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: Q9KQ12
#2: Protein
Flagellar basal-body rod protein FlgF


Mass: 26778.270 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: Q9KQ11
#3: Protein
Flagellar hook protein FlgE


Mass: 46880.289 Da / Num. of mol.: 17 / Source method: isolated from a natural source
Source: (natural) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: Q9KQ10
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: C1 (asymmetric)
3D reconstructionResolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77446 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 110.49 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002197962
ELECTRON MICROSCOPYf_angle_d0.4489132712
ELECTRON MICROSCOPYf_chiral_restr0.04215092
ELECTRON MICROSCOPYf_plane_restr0.003417914
ELECTRON MICROSCOPYf_dihedral_angle_d12.131435983

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