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- PDB-9yds: H-ring subunit FlgO and FlgP in Vibrio cholerae at assembled, ope... -

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Basic information

Entry
Database: PDB / ID: 9yds
TitleH-ring subunit FlgO and FlgP in Vibrio cholerae at assembled, opened state
Components
  • FlgO domain-containing protein
  • Lipoprotein
KeywordsMOTOR PROTEIN / In situ cryo-EM / sheathed flagellar motor / Vibrio cholerae / H-ring / assembled state
Function / homologyFlagellar protein FlgO / FlgO domain / FlgO protein / Flagellar protein FlgP / Prokaryotic membrane lipoprotein lipid attachment site profile. / FlgO domain-containing protein / Lipoprotein
Function and homology information
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 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: 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
Aa: Lipoprotein
Ab: FlgO domain-containing protein
Ac: Lipoprotein
Ad: FlgO domain-containing protein
Ae: Lipoprotein
Af: FlgO domain-containing protein
Ag: Lipoprotein
Ah: FlgO domain-containing protein
Ai: Lipoprotein
Aj: FlgO domain-containing protein
Ak: Lipoprotein
Al: FlgO domain-containing protein
Am: Lipoprotein
An: FlgO domain-containing protein
Ao: Lipoprotein
Ap: FlgO domain-containing protein
Aq: Lipoprotein
Ar: FlgO domain-containing protein
As: Lipoprotein
At: FlgO domain-containing protein
Au: Lipoprotein
Av: FlgO domain-containing protein
Aw: Lipoprotein
Ax: FlgO domain-containing protein
Ay: Lipoprotein
Az: FlgO domain-containing protein
Ba: Lipoprotein
Bb: FlgO domain-containing protein
Bc: Lipoprotein
Bd: FlgO domain-containing protein
Be: Lipoprotein
Bf: FlgO domain-containing protein
Bg: Lipoprotein
Bh: FlgO domain-containing protein
Bi: Lipoprotein
Bj: FlgO domain-containing protein
Bk: Lipoprotein
Bl: FlgO domain-containing protein
Bm: Lipoprotein
Bn: FlgO domain-containing protein
Bo: Lipoprotein
Bp: FlgO domain-containing protein
Bq: Lipoprotein
Br: FlgO domain-containing protein
Bs: Lipoprotein
Bt: FlgO domain-containing protein
Bu: Lipoprotein
Bv: FlgO domain-containing protein
Bw: Lipoprotein
Bx: FlgO domain-containing protein
By: Lipoprotein
Bz: FlgO domain-containing protein
Ca: Lipoprotein
Cb: FlgO domain-containing protein
Cc: Lipoprotein
Cd: FlgO domain-containing protein
Ce: Lipoprotein
Cf: FlgO domain-containing protein
Cg: Lipoprotein
Ch: FlgO domain-containing protein
Ci: Lipoprotein
Cj: FlgO domain-containing protein
Ck: Lipoprotein
Cl: FlgO domain-containing protein
Cm: Lipoprotein
Cn: FlgO domain-containing protein
Co: Lipoprotein
Cp: FlgO domain-containing protein
Cq: Lipoprotein
Cr: FlgO domain-containing protein
Cs: Lipoprotein
Ct: FlgO domain-containing protein
Cu: Lipoprotein
Cv: FlgO domain-containing protein
Cw: Lipoprotein
Cx: FlgO domain-containing protein
Cy: Lipoprotein
Cz: FlgO domain-containing protein
Da: Lipoprotein
Db: FlgO domain-containing protein
Dc: Lipoprotein
Dd: FlgO domain-containing protein
De: Lipoprotein
Df: FlgO domain-containing protein
Dg: Lipoprotein
Dh: FlgO domain-containing protein
Di: Lipoprotein
Dj: FlgO domain-containing protein
Dk: Lipoprotein
Dl: FlgO domain-containing protein
Dm: Lipoprotein
Dn: FlgO domain-containing protein
Do: Lipoprotein
Dp: FlgO domain-containing protein
Dq: Lipoprotein
Dr: FlgO domain-containing protein
Ds: Lipoprotein
Dt: FlgO domain-containing protein
Du: Lipoprotein
Dv: FlgO domain-containing protein
Dw: Lipoprotein
Dx: FlgO domain-containing protein
Dy: Lipoprotein
Dz: FlgO domain-containing protein
Ea: Lipoprotein
Eb: FlgO domain-containing protein
Ec: Lipoprotein
Ed: FlgO domain-containing protein
Ee: Lipoprotein
Ef: FlgO domain-containing protein
Eg: Lipoprotein
Eh: FlgO domain-containing protein
Ei: Lipoprotein
Ej: FlgO domain-containing protein
Ek: Lipoprotein
El: FlgO domain-containing protein


Theoretical massNumber of molelcules
Total (without water)1,937,873116
Polymers1,937,873116
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 ...
Lipoprotein / FlgP


Mass: 11848.299 Da / Num. of mol.: 58 / Source method: isolated from a natural source
Source: (natural) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: Q9KQ01
#2: Protein ...
FlgO domain-containing protein / FlgI


Mass: 21563.299 Da / Num. of mol.: 58 / Source method: isolated from a natural source
Source: (natural) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: Q9KQ00
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: C58 (58 fold cyclic)
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35317 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 61.53 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0022135952
ELECTRON MICROSCOPYf_angle_d0.4866183512
ELECTRON MICROSCOPYf_chiral_restr0.043220648
ELECTRON MICROSCOPYf_plane_restr0.003524070
ELECTRON MICROSCOPYf_dihedral_angle_d11.107850808

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