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

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Basic information

Entry
Database: PDB / ID: 9yec
TitleLPHT-ring in Vibrio cholerae at disassembled, closed state
Components
  • (Sodium-type flagellar protein ...) x 2
  • Flagellar L-ring protein
  • Flagellar P-ring protein
  • Flagellar protein FlgT
  • Lipoprotein
KeywordsMOTOR PROTEIN / In situ cryo-EM / sheathed flagellar motor / Vibrio cholerae / T-ring / MotX / C26 assembled 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 / : / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / : / OmpA-like domain profile. / OmpA family / OmpA-like domain / OmpA-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Sodium-type flagellar protein MotX / Flagellar protein FlgT / Lipoprotein / 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: 3.57 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

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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
Ea: Sodium-type flagellar protein MotX
Eb: Sodium-type flagellar protein MotX
Ec: Sodium-type flagellar protein MotX
Ed: Sodium-type flagellar protein MotX
Ee: Sodium-type flagellar protein MotX
Ef: Sodium-type flagellar protein MotX
Eg: Sodium-type flagellar protein MotX
Eh: Sodium-type flagellar protein MotX
Ei: Sodium-type flagellar protein MotX
Ej: Sodium-type flagellar protein MotX
Ek: Sodium-type flagellar protein MotX
El: Sodium-type flagellar protein MotX
Em: Sodium-type flagellar protein MotX
En: Sodium-type flagellar protein MotX
Eo: Sodium-type flagellar protein MotX
Ep: Sodium-type flagellar protein MotX
Eq: Sodium-type flagellar protein MotX
Er: Sodium-type flagellar protein MotX
Es: Sodium-type flagellar protein MotX
Et: Sodium-type flagellar protein MotX
Eu: Sodium-type flagellar protein MotX
Ev: Sodium-type flagellar protein MotX
Ew: Sodium-type flagellar protein MotX
Ex: Sodium-type flagellar protein MotX
Ey: Sodium-type flagellar protein MotX
Ez: Sodium-type flagellar protein MotX
Fa: Lipoprotein
Fb: Lipoprotein
Fc: Lipoprotein
Fd: Lipoprotein
Fe: Lipoprotein
Ff: Lipoprotein
Fg: Lipoprotein
Fh: Lipoprotein
Fi: Lipoprotein
Fj: Lipoprotein
Fk: Lipoprotein
Fl: Lipoprotein
Fm: Lipoprotein
Fn: Lipoprotein
Fo: Lipoprotein
Fp: Lipoprotein
Fq: Lipoprotein
Fr: Lipoprotein
Fs: Lipoprotein
Ft: Lipoprotein
Fu: Lipoprotein
Fv: Lipoprotein
Fw: Lipoprotein
Fx: Lipoprotein
Fy: Lipoprotein
Fz: Lipoprotein
Ga: Lipoprotein
Gb: Lipoprotein
Gc: Lipoprotein
Gd: Lipoprotein
Ge: Lipoprotein
Gf: Lipoprotein
Gg: Lipoprotein
Gh: Lipoprotein
Gi: Lipoprotein
Gj: Lipoprotein
Gk: Lipoprotein
Gl: Lipoprotein
Gm: Lipoprotein
Gn: Lipoprotein
Go: Lipoprotein
Gp: Lipoprotein
Gq: Lipoprotein
Gr: Lipoprotein
Gs: Lipoprotein
Gt: Lipoprotein
Gu: Lipoprotein
Gv: Lipoprotein
Gw: Lipoprotein
Gx: Lipoprotein
Gy: Lipoprotein
Gz: Lipoprotein


Theoretical massNumber of molelcules
Total (without water)5,165,409182
Polymers5,165,409182
Non-polymers00
Water00
1


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

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Components

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Protein , 4 types, 130 molecules AaAbAcAdAeAfAgAhAiAjAkAlAmAnAoApAqArAsAtAuAvAwAxAyAzBaBbBcBd...

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


Mass: 27541.480 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: 37694.059 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: 42647.734 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
#6: Protein ...
Lipoprotein


Mass: 16459.971 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: Q9KQ01

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Sodium-type flagellar protein ... , 2 types, 52 molecules DaDbDcDdDeDfDgDhDiDjDkDlDmDnDoDpDqDrDsDtDuDvDwDxDyDzEaEbEcEd...

#4: Protein ...
Sodium-type flagellar protein MotY


Mass: 33587.746 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 ...
Sodium-type flagellar protein MotX


Mass: 24278.615 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: Q9KNX9

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Details

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: 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: 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 / Cs: 2.7 mm / C2 aperture diameter: 100 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: C13 (13 fold cyclic)
3D reconstructionResolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25553 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 136.35 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002284024
ELECTRON MICROSCOPYf_angle_d0.4596384878
ELECTRON MICROSCOPYf_chiral_restr0.041943654
ELECTRON MICROSCOPYf_plane_restr0.003750661
ELECTRON MICROSCOPYf_dihedral_angle_d10.8008105677

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