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- EMDB-63394: The chimeric flagellar motor complex between MotA1B1 from Paeniba... -

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Basic information

Entry
Database: EMDB / ID: EMD-63394
TitleThe chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli, state 3
Map data
Sample
  • Complex: The chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli
    • Protein or peptide: Flagellar motor protein MotA
    • Protein or peptide: Chimeric B subunit of MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E. coli
KeywordsFlagellar / motility / Paenibacillus / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum-dependent swarming motility / chemotaxis / protein transport / plasma membrane
Similarity search - Function
Motility protein A, N-terminal / Motility protein A N-terminal / : / MotA/TolQ/ExbB proton channel / MotA/TolQ/ExbB proton channel family
Similarity search - Domain/homology
Flagellar motor protein MotA
Similarity search - Component
Biological speciesPaenibacillus sp. TCA20 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsOnoe S / Nishikino T / Kinoshita M / Kishikawa J / Kato T
Funding support Japan, 2 items
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, 2025-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63394.png

Downloads & links

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Map

FileDownload / File: emd_63394.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 256 pix.
= 225.28 Å		0.88 Å/pix.
x 256 pix.
= 225.28 Å		0.88 Å/pix.
x 256 pix.
= 225.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21
Minimum - Maximum-0.47342265 - 0.8178104
Average (Standard dev.)0.0007887125 (±0.03143675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 225.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63394_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63394_half_map_2.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The chimeric flagellar motor complex between MotA1B1 from Paeniba...

EntireName: The chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli
Components
  • Complex: The chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli
    • Protein or peptide: Flagellar motor protein MotA
    • Protein or peptide: Chimeric B subunit of MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E. coli

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Supramolecule #1: The chimeric flagellar motor complex between MotA1B1 from Paeniba...

SupramoleculeName: The chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Paenibacillus sp. TCA20 (bacteria)
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: Flagellar motor protein MotA

MacromoleculeName: Flagellar motor protein MotA / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Paenibacillus sp. TCA20 (bacteria)
Molecular weightTheoretical: 26.573006 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDIATLIGLI AGAVAIIGGF LWEGGQITGL FQGTAALIVF GGTIAAVLIS YPMHRIRTLP AGIKLAFKPN RSEVNEWLED IVEMSMVAR REGVLALEQK VLDHPNIFLR EGIQLVVDGT DQPIVRQIME LDIDAKEQEH DNYAKLFESA GSYAPTMGII G TVMGLIQV ...String:
MDIATLIGLI AGAVAIIGGF LWEGGQITGL FQGTAALIVF GGTIAAVLIS YPMHRIRTLP AGIKLAFKPN RSEVNEWLED IVEMSMVAR REGVLALEQK VLDHPNIFLR EGIQLVVDGT DQPIVRQIME LDIDAKEQEH DNYAKLFESA GSYAPTMGII G TVMGLIQV LGHLTDPSQL GPSIAVAFIA TLYGVASANL IFLPIASKIR AKSAEEILVM EMILEGVLSV QNGDNALLVR KK LNTYIT

UniProtKB: Flagellar motor protein MotA

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Macromolecule #2: Chimeric B subunit of MotA1B1 from Paenibacillus sp. TCA20 and Mo...

MacromoleculeName: Chimeric B subunit of MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E. coli
type: protein_or_peptide / ID: 2 / Details: 6xHis on C-terminal is purification tag / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Paenibacillus sp. TCA20 (bacteria)
Molecular weightTheoretical: 5.71358 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GSPHDRWMIT YADLITLLLI FFVMMYAMSR LDASKYEEVT SSLQTTFQS

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: CEOS cs corrector / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 3129 / Average exposure time: 3.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.295 µm / Calibrated defocus min: 0.171 µm / Calibrated magnification: 56818 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.073 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 765007
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.8) / Number images used: 54290
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.8)
Final 3D classificationNumber classes: 6 / Avg.num./class: 40000 / Software - Name: cryoSPARC (ver. 3.8)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9luc:
The chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli, state 3

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