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- PDB-9yfg: Flagellar outer membrane complex in Vibrio cholerae at disassembl... -

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Basic information

Entry
Database: PDB / ID: 9yfg
TitleFlagellar outer membrane complex 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
  • FlgO domain-containing protein
  • FlgP
  • Lipoprotein
KeywordsMOTOR PROTEIN / Vibrio cholerae / in situ cryo-EM / closed / flagellar outer membrane complex
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 protein FlgO / FlgO domain / FlgO protein / 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 ...Flagellar protein FlgO / FlgO domain / FlgO protein / 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 / FlgO domain-containing protein / 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: 3.55 Å
AuthorsGuo, W. / Yue, J. / Liu, J.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI189907 United States
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
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI102584 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. / Jun, L.
History
DepositionSep 25, 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
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: FlgP
Fb: FlgP
Fc: FlgP
Fd: FlgP
Fe: FlgP
Ff: FlgP
Fg: FlgP
Fh: FlgP
Fi: FlgP
Fj: FlgP
Fk: FlgP
Fl: FlgP
Fm: FlgP
Fn: FlgP
Fo: FlgP
Fp: FlgP
Fq: FlgP
Fr: FlgP
Fs: FlgP
Ft: FlgP
Fu: FlgP
Fv: FlgP
Fw: FlgP
Fx: FlgP
Fy: FlgP
Fz: FlgP
Ga: FlgP
Gb: FlgP
Gc: FlgP
Gd: FlgP
Ge: FlgP
Gf: FlgP
Gg: FlgP
Gh: FlgP
Gi: FlgP
Gj: FlgP
Gk: FlgP
Gl: FlgP
Gm: FlgP
Gn: FlgP
Go: FlgP
Gp: FlgP
Gq: FlgP
Gr: FlgP
Gs: FlgP
Gt: FlgP
Gu: FlgP
Gv: FlgP
Gw: FlgP
Gx: FlgP
Gy: FlgP
Gz: FlgP
Ha: Lipoprotein
Hb: FlgO domain-containing protein
Hc: Lipoprotein
Hd: FlgO domain-containing protein
He: Lipoprotein
Hf: FlgO domain-containing protein
Hg: Lipoprotein
Hh: FlgO domain-containing protein
Hi: Lipoprotein
Hj: FlgO domain-containing protein
Hk: Lipoprotein
Hl: FlgO domain-containing protein
Hm: Lipoprotein
Hn: FlgO domain-containing protein
Ho: Lipoprotein
Hp: FlgO domain-containing protein
Hq: Lipoprotein
Hr: FlgO domain-containing protein
Hs: Lipoprotein
Ht: FlgO domain-containing protein
Hu: Lipoprotein
Hv: FlgO domain-containing protein
Hw: Lipoprotein
Hx: FlgO domain-containing protein
Hy: Lipoprotein
Hz: FlgO domain-containing protein
Ia: Lipoprotein
Ib: FlgO domain-containing protein
Ic: Lipoprotein
Id: FlgO domain-containing protein
Ie: Lipoprotein
If: FlgO domain-containing protein
Ig: Lipoprotein
Ih: FlgO domain-containing protein
Ii: Lipoprotein
Ij: FlgO domain-containing protein
Ik: Lipoprotein
Il: FlgO domain-containing protein
Im: Lipoprotein
In: FlgO domain-containing protein
Io: Lipoprotein
Ip: FlgO domain-containing protein
Iq: Lipoprotein
Ir: FlgO domain-containing protein
Is: Lipoprotein
It: FlgO domain-containing protein
Iu: Lipoprotein
Iv: FlgO domain-containing protein
Iw: Lipoprotein
Ix: FlgO domain-containing protein
Iy: Lipoprotein
Iz: FlgO domain-containing protein
Ja: Lipoprotein
Jb: FlgO domain-containing protein
Jc: Lipoprotein
Jd: FlgO domain-containing protein
Je: Lipoprotein
Jf: FlgO domain-containing protein
Jg: Lipoprotein
Jh: FlgO domain-containing protein
Ji: Lipoprotein
Jj: FlgO domain-containing protein
Jk: Lipoprotein
Jl: FlgO domain-containing protein
Jm: Lipoprotein
Jn: FlgO domain-containing protein
Jo: Lipoprotein
Jp: FlgO domain-containing protein
Jq: Lipoprotein
Jr: FlgO domain-containing protein
Js: Lipoprotein
Jt: FlgO domain-containing protein
Ju: Lipoprotein
Jv: FlgO domain-containing protein
Jw: Lipoprotein
Jx: FlgO domain-containing protein
Jy: Lipoprotein
Jz: FlgO domain-containing protein
Ka: Lipoprotein
Kb: FlgO domain-containing protein
Kc: Lipoprotein
Kd: FlgO domain-containing protein
Ke: Lipoprotein
Kf: FlgO domain-containing protein
Kg: Lipoprotein
Kh: FlgO domain-containing protein
Ki: Lipoprotein
Kj: FlgO domain-containing protein
Kk: Lipoprotein
Kl: FlgO domain-containing protein
Km: Lipoprotein
Kn: FlgO domain-containing protein
Ko: Lipoprotein
Kp: FlgO domain-containing protein
Kq: Lipoprotein
Kr: FlgO domain-containing protein
Ks: Lipoprotein
Kt: FlgO domain-containing protein
Ku: Lipoprotein
Kv: FlgO domain-containing protein
Kw: Lipoprotein
Kx: FlgO domain-containing protein
Ky: Lipoprotein
Kz: FlgO domain-containing protein
La: Lipoprotein
Lb: FlgO domain-containing protein
Lc: Lipoprotein
Ld: FlgO domain-containing protein
Le: Lipoprotein
Lf: FlgO domain-containing protein
Lg: Lipoprotein
Lh: FlgO domain-containing protein
Li: Lipoprotein
Lj: FlgO domain-containing protein
Lk: Lipoprotein
Ll: FlgO domain-containing protein


Theoretical massNumber of molelcules
Total (without water)5,969,923298
Polymers5,969,923298
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 5 types, 194 molecules AaAbAcAdAeAfAgAhAiAjAkAlAmAnAoApAqArAsAtAuAvAwAxAyAzBaBbBcBd...

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


Mass: 24256.520 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: flgH, VC_2194
Production host: 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 genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: flgI, VC_2193
Production host: 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 genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: VC_2208
Production host: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: Q9KPZ9
#7: Protein ...
Lipoprotein / FlgP


Mass: 11947.430 Da / Num. of mol.: 58
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: VC_2206
Production host: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: Q9KQ01
#8: Protein ...
FlgO domain-containing protein


Mass: 21395.104 Da / Num. of mol.: 58
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: VC_2207
Production host: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: Q9KQ00

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

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


Mass: 31207.955 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: VC_1008
Production host: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: Q9KT95
#5: Protein ...
Sodium-type flagellar protein MotX


Mass: 21244.137 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: VC_2601
Production host: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: Q9KNX9

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Protein/peptide , 1 types, 52 molecules FaFbFcFdFeFfFgFhFiFjFkFlFmFnFoFpFqFrFsFtFuFvFwFxFyFzGaGbGcGd...

#6: Protein/peptide ...
FlgP


Mass: 1506.766 Da / Num. of mol.: 52
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Production host: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)

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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: FLOOD BEAM
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
IDNameCategory
1Topazparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 177296 / Symmetry type: POINT

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