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- PDB-9lub: The chimeric flagellar motor complex between MotA1B1 from Paeniba... -

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Basic information

Entry
Database: PDB / ID: 9lub
TitleThe chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli, state 2
Components
  • Chimeric B subunit of MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E. coli,Motility protein B
  • Flagellar motor protein MotA
KeywordsMOTOR PROTEIN / Flagellar / motility / Paenibacillus
Function / homology
Function and homology information


bacterial-type flagellum stator complex / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / proton channel activity / bacterial-type flagellum-dependent cell motility / proton transmembrane transport / chemotaxis / protein transport / plasma membrane
Similarity search - Function
Motility protein A, N-terminal / Motility protein A N-terminal / : / Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / MotA/TolQ/ExbB proton channel / MotA/TolQ/ExbB proton channel family / : / OmpA-like domain profile. / OmpA-like domain superfamily ...Motility protein A, N-terminal / Motility protein A N-terminal / : / Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / MotA/TolQ/ExbB proton channel / MotA/TolQ/ExbB proton channel family / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain
Similarity search - Domain/homology
Flagellar motor protein MotA / Motility protein B
Similarity search - Component
Biological speciesPaenibacillus sp. TCA20 (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsOnoe, S. / Nishikino, T. / Kinoshita, M. / Kishikawa, J. / Kato, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101XXX. Japan
Japan Society for the Promotion of Science (JSPS)JP23K14157 Japan
CitationJournal: Biomolecules / Year: 2025
Title: Cryo-EM Structure of the Flagellar Motor Complex from sp. TCA20.
Authors: Sakura Onoe / Tatsuro Nishikino / Miki Kinoshita / Norihiro Takekawa / Tohru Minamino / Katsumi Imada / Keiichi Namba / Jun-Ichi Kishikawa / Takayuki Kato /
Abstract: The bacterial flagellum, a complex nanomachine composed of numerous proteins, is utilized by bacteria for swimming in various environments and plays a crucial role in their survival and infection. ...The bacterial flagellum, a complex nanomachine composed of numerous proteins, is utilized by bacteria for swimming in various environments and plays a crucial role in their survival and infection. The flagellar motor is composed of a rotor and stator complexes, with each stator unit functioning as an ion channel that converts flow from outside of cell membrane into rotational motion. sp. TCA20 was discovered in a hot spring, and a structural analysis was conducted on the stator complex using cryo-electron microscopy to elucidate its function. Two of the three structures (Classes 1 and 3) were found to have structural properties typical for other stator complexes. In contrast, in Class 2 structures, the pentamer ring of the A subunits forms a C-shape, with lauryl maltose neopentyl glycol (LMNG) bound to the periplasmic side of the interface between the A and B subunits. This interface is conserved in all stator complexes, suggesting that hydrophobic ligands and lipids can bind to this interface, a feature that could potentially be utilized in the development of novel antibiotics aimed at regulating cell motility and infection.
History
DepositionFeb 8, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellar motor protein MotA
B: Flagellar motor protein MotA
C: Flagellar motor protein MotA
D: Flagellar motor protein MotA
E: Flagellar motor protein MotA
F: Chimeric B subunit of MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E. coli,Motility protein B
G: Chimeric B subunit of MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E. coli,Motility protein B


Theoretical massNumber of molelcules
Total (without water)213,3667
Polymers213,3667
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Flagellar motor protein MotA


Mass: 28568.139 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. TCA20 (bacteria) / Gene: TCA2_3717 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A069DFV9
#2: Protein Chimeric B subunit of MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E. coli,Motility protein B / Chemotaxis protein MotB


Mass: 35262.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 6xHis on C terminal is purification tag
Source: (gene. exp.) Paenibacillus sp. TCA20 (bacteria), (gene. exp.) Escherichia coli (E. coli)
Gene: motB, b1889, JW1878 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AF06
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.15 MDa / Experimental value: NO
Source (natural)Organism: Paenibacillus sp. TCA20 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 magnification: 59000 X / Calibrated magnification: 56818 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 175 nm / Calibrated defocus max: 3295 nm / Cs: 0.073 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3129
EM imaging opticsEnergyfilter name: GIF Bioquantum / Chromatic aberration corrector: CEOS Cs corrector / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.8particle selection
2SerialEMimage acquisition
4cryoSPARC3.8CTF correction
7Cootmodel fitting
9Servalcatmodel refinement
10cryoSPARC3.8initial Euler assignment
11cryoSPARC3.8final Euler assignment
12cryoSPARC3.8classification
13cryoSPARC3.83D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 765007
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69957 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementResolution: 3.3→3.3 Å / Cor.coef. Fo:Fc: 0.734 / SU B: 28.645 / SU ML: 0.422 / ESU R: 1.095
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.38422 --
obs0.38422 55733 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 92.348 Å2
Refinement stepCycle: 1 / Total: 10116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.01210279
ELECTRON MICROSCOPYr_bond_other_d00.01610006
ELECTRON MICROSCOPYr_angle_refined_deg1.561.62613941
ELECTRON MICROSCOPYr_angle_other_deg0.5161.54923195
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.27751319
ELECTRON MICROSCOPYr_dihedral_angle_2_deg18.845549
ELECTRON MICROSCOPYr_dihedral_angle_3_deg20.965101818
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0850.21682
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0211490
ELECTRON MICROSCOPYr_gen_planes_other0.0010.021890
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it9.3698.4125295
ELECTRON MICROSCOPYr_mcbond_other9.3648.4115295
ELECTRON MICROSCOPYr_mcangle_it15.51512.6026605
ELECTRON MICROSCOPYr_mcangle_other15.51512.6066606
ELECTRON MICROSCOPYr_scbond_it12.74310.3924984
ELECTRON MICROSCOPYr_scbond_other12.74210.3954985
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other21.79814.8887337
ELECTRON MICROSCOPYr_long_range_B_refined31.19641622
ELECTRON MICROSCOPYr_long_range_B_other31.19541618
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.087 4085 -
obs--100 %

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