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- EMDB-60585: Bacterial flagellar sodium-driven stator PomA5PomB2(D24N) with 10... -

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Basic information

Entry
Database: EMDB / ID: EMD-60585
TitleBacterial flagellar sodium-driven stator PomA5PomB2(D24N) with 100 mM KCl
Map datapostprocessed map
Sample
  • Complex: Bacterial flagellar sodium-driven stator PomA5PomB2(D24N) with 100 mM KCl
    • Protein or peptide: PomB
    • Protein or peptide: Chemotaxis protein PomA
  • Ligand: water
Keywordsbacterial flagellar stator unit / sodium ion transport / membrane protein complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum-dependent swarming motility / proton transmembrane transport / chemotaxis / plasma membrane
Similarity search - Function
Flagellar motor protein MotA, conserved site / Flagellar motor protein motA family signature. / : / 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 ...Flagellar motor protein MotA, conserved site / Flagellar motor protein motA family signature. / : / 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
Chemotaxis protein PomA / PomB
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsNishikino T / Kishikawa J / Hirose M / Kato T / Imada K
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP20J00329 Japan
Japan Society for the Promotion of Science (JSPS)JP23K14157 Japan
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural insight into sodium ion pathway in the bacterial flagellar stator from marine .
Authors: Tatsuro Nishikino / Norihiro Takekawa / Jun-Ichi Kishikawa / Mika Hirose / Seiji Kojima / Michio Homma / Takayuki Kato / Katsumi Imada /
Abstract: Many bacteria swim in liquid or swarm on surface using the flagellum rotated by a motor driven by specific ion flow. The motor consists of the rotor and stator, and the stator converts the energy of ...Many bacteria swim in liquid or swarm on surface using the flagellum rotated by a motor driven by specific ion flow. The motor consists of the rotor and stator, and the stator converts the energy of ion flow to mechanical rotation. However, the ion pathway and the mechanism of stator rotation coupled with specific ion flow are still obscure. Here, we determined the structures of the sodium-driven stator of , namely PomAB, in the presence and absence of sodium ions and the structure with its specific inhibitor, phenamil, by cryo-electron microscopy. The structures and following functional analysis revealed the sodium ion pathway, the mechanism of ion selectivity, and the inhibition mechanism by phenamil. We propose a model of sodium ion flow coupled with the stator rotation based on the structures. This work provides insights into the molecular mechanisms of ion specificity and conversion of the electrochemical potential into mechanical functions.
#1: Journal: Proc.Natl.Acad.Sci.USA
Title: Structural insight into sodium ion pathway in the bacterial flagellar stator from marine Vibrio
Authors: Nishikino T / Takekawa N / Kishikawa J / Hirose M / Kojima S / Homma M / Kato T / Imada K
History
DepositionJun 18, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60585.png

Downloads & links

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Map

FileDownload / File: emd_60585.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 150 pix.
= 202.5 Å		1.35 Å/pix.
x 150 pix.
= 202.5 Å		1.35 Å/pix.
x 150 pix.
= 202.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.27624825 - 0.42158258
Average (Standard dev.)0.00031566762 (±0.012548389)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 202.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60585_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map2

Fileemd_60585_half_map_1.map
Annotationhalf map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map1

Fileemd_60585_half_map_2.map
Annotationhalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacterial flagellar sodium-driven stator PomA5PomB2(D24N) with 10...

EntireName: Bacterial flagellar sodium-driven stator PomA5PomB2(D24N) with 100 mM KCl
Components
  • Complex: Bacterial flagellar sodium-driven stator PomA5PomB2(D24N) with 100 mM KCl
    • Protein or peptide: PomB
    • Protein or peptide: Chemotaxis protein PomA
  • Ligand: water

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Supramolecule #1: Bacterial flagellar sodium-driven stator PomA5PomB2(D24N) with 10...

SupramoleculeName: Bacterial flagellar sodium-driven stator PomA5PomB2(D24N) with 100 mM KCl
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: VIO5
Molecular weightTheoretical: 210 KDa

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Macromolecule #1: PomB

MacromoleculeName: PomB / type: protein_or_peptide / ID: 1 / Details: 6 His residues on C-terminal are purification tag / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: VIO5
Molecular weightTheoretical: 36.329051 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDDEDNKCDC PPPGLPLWMG TFANLMSLLM CFFVLLLSFS EMDVLKFKQI AGSMKFAFGV QNQLEVKDIP KGTSIIAQEF RPGRPEPTP IDVIMQQTMD ITQQTLEFHE GESDRAGGTK RDEGKLTGGQ SPATSTQNNE SAEADMQQQQ SKEMSQEMET L MESIKKAL ...String:
MDDEDNKCDC PPPGLPLWMG TFANLMSLLM CFFVLLLSFS EMDVLKFKQI AGSMKFAFGV QNQLEVKDIP KGTSIIAQEF RPGRPEPTP IDVIMQQTMD ITQQTLEFHE GESDRAGGTK RDEGKLTGGQ SPATSTQNNE SAEADMQQQQ SKEMSQEMET L MESIKKAL EREIEQGAIE VENLGQQIVI RMREKGAFPE GSAFLQPKFR PLVRQIAELV KDVPGIVRVS GHTDNRPLDS EL YRSNWDL SSQRAVSVAQ EMEKVRGFSH QRLRVRGMAD TEPLLPNDSD DNRALNRRVE ISIMQGEPLY SEEVPVIQHH HHH H

UniProtKB: PomB

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Macromolecule #2: Chemotaxis protein PomA

MacromoleculeName: Chemotaxis protein PomA / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: VIO5
Molecular weightTheoretical: 27.283031 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDLATLLGLI GGFAFVIMAM VLGGSIGMFV DVTSILIVVG GSIFVVLMKF TMGQFFGATK IAGKAFMFKA DEPEDLIAKI VEMADAARK GGFLALEEME INNTFMQKGI DLLVDGHDAD VVRAALKKDI ALTDERHTQG TGVFRAFGDV APAMGMIGTL V GLVAMLSN ...String:
MDLATLLGLI GGFAFVIMAM VLGGSIGMFV DVTSILIVVG GSIFVVLMKF TMGQFFGATK IAGKAFMFKA DEPEDLIAKI VEMADAARK GGFLALEEME INNTFMQKGI DLLVDGHDAD VVRAALKKDI ALTDERHTQG TGVFRAFGDV APAMGMIGTL V GLVAMLSN MDDPKAIGPA MAVALLTTLY GAILSNMVFF PIADKLSLRR DQETLNRRLI MDGVLAIQDG QNPRVIDSYL KN YLNEGKR ALEIDE

UniProtKB: Chemotaxis protein PomA

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 3 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 8
Component:
ConcentrationFormulaName
100.0 mMKClPotassium chloride
20.0 mMC4H11NO3Tris-HCl
0.0025 % (w/v)C47H88C22LMNG
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 13551 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 724089
Startup modelType of model: EMDB MAP
EMDB ID:

60580

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 325940
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final 3D classificationSoftware - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8zyv


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8zz0:
Bacterial flagellar sodium-driven stator PomA5PomB2(D24N) with 100 mM KCl

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