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- PDB-9yed: T-ring-PomB complex in Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 9yed
TitleT-ring-PomB complex in Vibrio cholerae
Components
  • Chemotaxis protein PomB
  • Sodium-type flagellar protein MotX
  • Sodium-type flagellar protein MotY
KeywordsMOTOR PROTEIN / In situ cryo-EM / sheathed flagellar motor / Vibrio cholerae / T-ring / PomB / assembled state
Function / homology
Function and homology information


bacterial-type flagellum stator complex / bacterial-type flagellum-dependent cell motility / cell outer membrane
Similarity search - Function
MotY N-terminal domain / MotY N-terminal domain / : / Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / : / OmpA-like domain profile. ...MotY N-terminal domain / MotY N-terminal domain / : / Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / : / OmpA-like domain profile. / OmpA family / OmpA-like domain / OmpA-like domain superfamily / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Sodium-type flagellar protein MotX / Sodium-type flagellar protein MotY / Chemotaxis protein PomB
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.98 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
AP1: Sodium-type flagellar protein MotX
BP1: Sodium-type flagellar protein MotY
CP1: Chemotaxis protein PomB
DP1: Chemotaxis protein PomB
EP1: Sodium-type flagellar protein MotX
FP1: Sodium-type flagellar protein MotY


Theoretical massNumber of molelcules
Total (without water)141,1596
Polymers141,1596
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "E"
d_2ens_1chain "A"
d_1ens_2chain "B"
d_2ens_2chain "F"
d_1ens_3chain "C"
d_2ens_3chain "D"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1ALAALATRPTRPEP1E24 - 2111 - 188
d_2ens_1ALAALATRPTRPAP1A24 - 2111 - 188
d_1ens_2LEULEUVALVALBP1B23 - 2941 - 272
d_2ens_2LEULEUVALVALFP1F23 - 2941 - 272
d_1ens_3GLNGLNLEULEUCP1C146 - 3001 - 155
d_2ens_3GLNGLNLEULEUDP1D146 - 3001 - 155

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.999280474743, -0.0175306625729, -0.0336334456672), (0.0168512691765, 0.999650321237, -0.0203781740519), (0.0339789276587, 0.0197967451947, 0.999226461497)-22.6572506984, -13.6565437359, -11.4333899519
2given(0.986756398869, 0.162205468874, 0.00109323345371), (-0.162130883388, 0.986048523574, 0.0377079011577), (0.00503844655457, -0.0373857596609, 0.99928820619)6.06576860978, 36.7343209272, 6.01387514257
3given(-0.96415204282, -0.120279041492, -0.236524397269), (-0.139288773904, -0.529275769572, 0.836938347316), (-0.22585277459, 0.839881010573, 0.493548794233)423.97211034, 155.79241407, -21.6370690882

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Components

#1: Protein Sodium-type flagellar protein MotX


Mass: 21729.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: Q9KNX9
#2: Protein Sodium-type flagellar protein MotY


Mass: 31307.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: Q9KT95
#3: Protein Chemotaxis protein PomB


Mass: 17542.775 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
References: UniProt: Q9KTK9
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 / 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: 4.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 697164 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 146.95 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001910110
ELECTRON MICROSCOPYf_angle_d0.51613674
ELECTRON MICROSCOPYf_chiral_restr0.04091480
ELECTRON MICROSCOPYf_plane_restr0.00341820
ELECTRON MICROSCOPYf_dihedral_angle_d12.5893890
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2EEP1ELECTRON MICROSCOPYNCS constraints5.09404644698E-11
ens_2d_2BBP1ELECTRON MICROSCOPYNCS constraints6.0446599132E-13
ens_3d_2CCP1ELECTRON MICROSCOPYNCS constraints1.65348989708E-12

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