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- PDB-9ydt: LPHT-ring in Vibrio cholerae at disassembled, closed state -

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Basic information

Entry
Database: PDB / ID: 9ydt
TitleLPHT-ring in Vibrio cholerae at disassembled, closed state
Components
  • Flagellar L-ring protein
  • Flagellar P-ring protein
  • Flagellar assembly lipoprotein FlgP
  • Flagellar protein FlgT
  • Sodium-type flagellar protein MotY
KeywordsMOTOR PROTEIN / In situ cryo-EM / sheathed flagellar motor / Vibrio cholerae / LP-ring / disassembled state / close state
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum basal body, distal rod, P ring / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / cell outer membrane / outer membrane-bounded periplasmic space / structural molecule activity
Similarity search - Function
Flagellar assembly protein T, N-terminal / Flagellar assembly protein T, middle domain / Flagellar assembly protein T, C-terminal / FlgT, C-terminal domain superfamily / Flagellar assembly protein T, C-terminal domain / Flagellar assembly protein T, middle domain / Flagellar assembly protein T, N-terminal domain / FlgT, N-terminal domain superfamily / MotY N-terminal domain / MotY N-terminal domain ...Flagellar assembly protein T, N-terminal / Flagellar assembly protein T, middle domain / Flagellar assembly protein T, C-terminal / FlgT, C-terminal domain superfamily / Flagellar assembly protein T, C-terminal domain / Flagellar assembly protein T, middle domain / Flagellar assembly protein T, N-terminal domain / FlgT, N-terminal domain superfamily / MotY N-terminal domain / MotY N-terminal domain / Flagellar protein FlgP / Flagellar L-ring protein / Flagellar L-ring protein / Flagellar P-ring protein / Flagellar P-ring protein / : / OmpA-like domain profile. / OmpA family / OmpA-like domain / OmpA-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Flagellar assembly lipoprotein FlgP / Flagellar protein FlgT / Flagellar L-ring protein / Flagellar P-ring protein / Sodium-type flagellar protein MotY
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 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. / Rajeev, K. / Jian, Y.
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: Flagellar L-ring protein
Ab: Flagellar L-ring protein
Ac: Flagellar L-ring protein
Ad: Flagellar L-ring protein
Ae: Flagellar L-ring protein
Af: Flagellar L-ring protein
Ag: Flagellar L-ring protein
Ah: Flagellar L-ring protein
Ai: Flagellar L-ring protein
Aj: Flagellar L-ring protein
Ak: Flagellar L-ring protein
Al: Flagellar L-ring protein
Am: Flagellar L-ring protein
An: Flagellar L-ring protein
Ao: Flagellar L-ring protein
Ap: Flagellar L-ring protein
Aq: Flagellar L-ring protein
Ar: Flagellar L-ring protein
As: Flagellar L-ring protein
At: Flagellar L-ring protein
Au: Flagellar L-ring protein
Av: Flagellar L-ring protein
Aw: Flagellar L-ring protein
Ax: Flagellar L-ring protein
Ay: Flagellar L-ring protein
Az: Flagellar L-ring protein
Ba: Flagellar P-ring protein
Bb: Flagellar P-ring protein
Bc: Flagellar P-ring protein
Bd: Flagellar P-ring protein
Be: Flagellar P-ring protein
Bf: Flagellar P-ring protein
Bg: Flagellar P-ring protein
Bh: Flagellar P-ring protein
Bi: Flagellar P-ring protein
Bj: Flagellar P-ring protein
Bk: Flagellar P-ring protein
Bl: Flagellar P-ring protein
Bm: Flagellar P-ring protein
Bn: Flagellar P-ring protein
Bo: Flagellar P-ring protein
Bp: Flagellar P-ring protein
Bq: Flagellar P-ring protein
Br: Flagellar P-ring protein
Bs: Flagellar P-ring protein
Bt: Flagellar P-ring protein
Bu: Flagellar P-ring protein
Bv: Flagellar P-ring protein
Bw: Flagellar P-ring protein
Bx: Flagellar P-ring protein
By: Flagellar P-ring protein
Bz: Flagellar P-ring protein
Ca: Flagellar protein FlgT
Cb: Flagellar protein FlgT
Cc: Flagellar protein FlgT
Cd: Flagellar protein FlgT
Ce: Flagellar protein FlgT
Cf: Flagellar protein FlgT
Cg: Flagellar protein FlgT
Ch: Flagellar protein FlgT
Ci: Flagellar protein FlgT
Cj: Flagellar protein FlgT
Ck: Flagellar protein FlgT
Cl: Flagellar protein FlgT
Cm: Flagellar protein FlgT
Cn: Flagellar protein FlgT
Co: Flagellar protein FlgT
Cp: Flagellar protein FlgT
Cq: Flagellar protein FlgT
Cr: Flagellar protein FlgT
Cs: Flagellar protein FlgT
Ct: Flagellar protein FlgT
Cu: Flagellar protein FlgT
Cv: Flagellar protein FlgT
Cw: Flagellar protein FlgT
Cx: Flagellar protein FlgT
Cy: Flagellar protein FlgT
Cz: Flagellar protein FlgT
Da: Sodium-type flagellar protein MotY
Db: Sodium-type flagellar protein MotY
Dc: Sodium-type flagellar protein MotY
Dd: Sodium-type flagellar protein MotY
De: Sodium-type flagellar protein MotY
Df: Sodium-type flagellar protein MotY
Dg: Sodium-type flagellar protein MotY
Dh: Sodium-type flagellar protein MotY
Di: Sodium-type flagellar protein MotY
Dj: Sodium-type flagellar protein MotY
Dk: Sodium-type flagellar protein MotY
Dl: Sodium-type flagellar protein MotY
Dm: Sodium-type flagellar protein MotY
Dn: Sodium-type flagellar protein MotY
Do: Sodium-type flagellar protein MotY
Dp: Sodium-type flagellar protein MotY
Dq: Sodium-type flagellar protein MotY
Dr: Sodium-type flagellar protein MotY
Ds: Sodium-type flagellar protein MotY
Dt: Sodium-type flagellar protein MotY
Du: Sodium-type flagellar protein MotY
Dv: Sodium-type flagellar protein MotY
Dw: Sodium-type flagellar protein MotY
Dx: Sodium-type flagellar protein MotY
Dy: Sodium-type flagellar protein MotY
Dz: Sodium-type flagellar protein MotY
Fa: Flagellar assembly lipoprotein FlgP
Fb: Flagellar assembly lipoprotein FlgP
Fc: Flagellar assembly lipoprotein FlgP
Fd: Flagellar assembly lipoprotein FlgP
Fe: Flagellar assembly lipoprotein FlgP
Ff: Flagellar assembly lipoprotein FlgP
Fg: Flagellar assembly lipoprotein FlgP
Fh: Flagellar assembly lipoprotein FlgP
Fi: Flagellar assembly lipoprotein FlgP
Fj: Flagellar assembly lipoprotein FlgP
Fk: Flagellar assembly lipoprotein FlgP
Fl: Flagellar assembly lipoprotein FlgP
Fm: Flagellar assembly lipoprotein FlgP
Fn: Flagellar assembly lipoprotein FlgP
Fo: Flagellar assembly lipoprotein FlgP
Fp: Flagellar assembly lipoprotein FlgP
Fq: Flagellar assembly lipoprotein FlgP
Fr: Flagellar assembly lipoprotein FlgP
Fs: Flagellar assembly lipoprotein FlgP
Ft: Flagellar assembly lipoprotein FlgP
Fu: Flagellar assembly lipoprotein FlgP
Fv: Flagellar assembly lipoprotein FlgP
Fw: Flagellar assembly lipoprotein FlgP
Fx: Flagellar assembly lipoprotein FlgP
Fy: Flagellar assembly lipoprotein FlgP
Fz: Flagellar assembly lipoprotein FlgP
Ga: Flagellar assembly lipoprotein FlgP
Gb: Flagellar assembly lipoprotein FlgP
Gc: Flagellar assembly lipoprotein FlgP
Gd: Flagellar assembly lipoprotein FlgP
Ge: Flagellar assembly lipoprotein FlgP
Gf: Flagellar assembly lipoprotein FlgP
Gg: Flagellar assembly lipoprotein FlgP
Gh: Flagellar assembly lipoprotein FlgP
Gi: Flagellar assembly lipoprotein FlgP
Gj: Flagellar assembly lipoprotein FlgP
Gk: Flagellar assembly lipoprotein FlgP
Gl: Flagellar assembly lipoprotein FlgP
Gm: Flagellar assembly lipoprotein FlgP
Gn: Flagellar assembly lipoprotein FlgP
Go: Flagellar assembly lipoprotein FlgP
Gp: Flagellar assembly lipoprotein FlgP
Gq: Flagellar assembly lipoprotein FlgP
Gr: Flagellar assembly lipoprotein FlgP
Gs: Flagellar assembly lipoprotein FlgP
Gt: Flagellar assembly lipoprotein FlgP
Gu: Flagellar assembly lipoprotein FlgP
Gv: Flagellar assembly lipoprotein FlgP
Gw: Flagellar assembly lipoprotein FlgP
Gx: Flagellar assembly lipoprotein FlgP
Gy: Flagellar assembly lipoprotein FlgP
Gz: Flagellar assembly lipoprotein FlgP


Theoretical massNumber of molelcules
Total (without water)3,501,121156
Polymers3,501,121156
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Flagellar L-ring protein / Basal body L-ring protein


Mass: 24256.520 Da / Num. of mol.: 26 / Source method: isolated from a natural source
Source: (natural) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: Q9KQ13
#2: Protein ...
Flagellar P-ring protein / Basal body P-ring protein


Mass: 35702.562 Da / Num. of mol.: 26 / Source method: isolated from a natural source
Source: (natural) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: Q9KQ14
#3: Protein ...
Flagellar protein FlgT


Mass: 39808.223 Da / Num. of mol.: 26 / Source method: isolated from a natural source
Source: (natural) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: Q9KPZ9
#4: Protein ...
Sodium-type flagellar protein MotY


Mass: 31307.084 Da / Num. of mol.: 26 / Source method: isolated from a natural source
Source: (natural) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: Q9KT95
#5: Protein/peptide ...
Flagellar assembly lipoprotein FlgP / Flagellar biosynthesis protein FlgP


Mass: 1792.062 Da / Num. of mol.: 52 / Source method: isolated from a natural source
Source: (natural) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: A0A2V4N6M7
Has protein modificationY

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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 DflhG / Type: ORGANELLE OR CELLULAR COMPONENT / 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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1600 nm / C2 aperture diameter: 2.7 µm
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: C26 (26 fold cyclic)
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31668 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 28.2 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0023244803
ELECTRON MICROSCOPYf_angle_d0.4906331721
ELECTRON MICROSCOPYf_chiral_restr0.043737882
ELECTRON MICROSCOPYf_plane_restr0.004243706
ELECTRON MICROSCOPYf_dihedral_angle_d10.546890831

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