[English] 日本語
Yorodumi
- EMDB-60636: Bacterial flagellar sodium-driven stator PomA5PomB2 with 100 mM N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60636
TitleBacterial flagellar sodium-driven stator PomA5PomB2 with 100 mM NaCl and 0.1 mM phenamil
Map datapostprocessed map
Sample
  • Complex: Bacterial flagellar sodium-driven stator PomA5PomB2 with 100 mM NaCl and 0.1 mM phenamil
    • Protein or peptide: PomB
    • Protein or peptide: Chemotaxis protein PomA
  • Ligand: SODIUM ION
  • Ligand: phenamil
  • Ligand: water
Keywordsbacterial flagellar stator unit / Phenamil / 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: 3.32 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 24, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_60636.png

Downloads & links

-
Map

FileDownload / File: emd_60636.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: 0.02
Minimum - Maximum-0.13043873 - 0.21159188
Average (Standard dev.)0.000023269879 (±0.00632215)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_60636_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map1

Fileemd_60636_half_map_1.map
Annotationhalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map2

Fileemd_60636_half_map_2.map
Annotationhalf map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Bacterial flagellar sodium-driven stator PomA5PomB2 with 100 mM N...

EntireName: Bacterial flagellar sodium-driven stator PomA5PomB2 with 100 mM NaCl and 0.1 mM phenamil
Components
  • Complex: Bacterial flagellar sodium-driven stator PomA5PomB2 with 100 mM NaCl and 0.1 mM phenamil
    • Protein or peptide: PomB
    • Protein or peptide: Chemotaxis protein PomA
  • Ligand: SODIUM ION
  • Ligand: phenamil
  • Ligand: water

-
Supramolecule #1: Bacterial flagellar sodium-driven stator PomA5PomB2 with 100 mM N...

SupramoleculeName: Bacterial flagellar sodium-driven stator PomA5PomB2 with 100 mM NaCl and 0.1 mM phenamil
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: VIO5
Molecular weightTheoretical: 210 KDa

-
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: 36.330035 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDDEDNKCDC PPPGLPLWMG TFADLMSLLM CFFVLLLSFS EMDVLKFKQI AGSMKFAFGV QNQLEVKDIP KGTSIIAQEF RPGRPEPTP IDVIMQQTMD ITQQTLEFHE GESDRAGGTK RDEGKLTGGQ SPATSTQNNE SAEADMQQQQ SKEMSQEMET L MESIKKAL ...String:
MDDEDNKCDC PPPGLPLWMG TFADLMSLLM 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

-
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

-
Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

-
Macromolecule #4: phenamil

MacromoleculeName: phenamil / type: ligand / ID: 4 / Number of copies: 1 / Formula: A1L2K
Molecular weightTheoretical: 305.723 Da

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
20.0 mMC4H11NO3Tris-HCl
0.005 % (w/v)C56H92O25GDN
1.0 % (w/v)C2H6SODMSO
0.1 mMC12H12ClN7O/CH3SO3HPhenamil methanesulfonate salt
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

-
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: 13874 / 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: 2.8000000000000003 µm / Nominal defocus min: 0.725 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 4573172
Startup modelType of model: EMDB MAP
EMDB ID:

60580

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 596902
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)

-
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-9ijm:
Bacterial flagellar sodium-driven stator PomA5PomB2 with 100 mM NaCl and 0.1 mM phenamil

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more