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- EMDB-16212: VaPomAB_LMNG -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-16212
TitleVaPomAB_LMNG
Map data
Sample
  • Complex: flagellar sodium-driven stator unit
    • Protein or peptide: Chemotaxis protein PomA
    • Protein or peptide: Flagellar motor protein,VaPomB
  • Protein or peptide: Chemotaxis protein PomA
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsFlagellar sodium-driven stator unit / MOTOR 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. / : / MotA/TolQ/ExbB proton channel / MotA/TolQ/ExbB proton channel family
Similarity search - Domain/homology
Chemotaxis protein PomA
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsHaidai H / Nicholas MIT
Funding support Denmark, 3 items
OrganizationGrant numberCountry
Novo Nordisk Foundation8123-00002B Denmark
Novo Nordisk FoundationNNF17OC0031006 Denmark
LundbeckfondenR347-2020-2429 Denmark
CitationJournal: Nat Commun / Year: 2023
Title: Ion selectivity and rotor coupling of the Vibrio flagellar sodium-driven stator unit.
Authors: Haidai Hu / Philipp F Popp / Mònica Santiveri / Aritz Roa-Eguiara / Yumeng Yan / Freddie J O Martin / Zheyi Liu / Navish Wadhwa / Yong Wang / Marc Erhardt / Nicholas M I Taylor /
Abstract: Bacteria swim using a flagellar motor that is powered by stator units. Vibrio spp. are highly motile bacteria responsible for various human diseases, the polar flagella of which are exclusively ...Bacteria swim using a flagellar motor that is powered by stator units. Vibrio spp. are highly motile bacteria responsible for various human diseases, the polar flagella of which are exclusively driven by sodium-dependent stator units (PomAB). However, how ion selectivity is attained, how ion transport triggers the directional rotation of the stator unit, and how the stator unit is incorporated into the flagellar rotor remained largely unclear. Here, we have determined by cryo-electron microscopy the structure of Vibrio PomAB. The electrostatic potential map uncovers sodium binding sites, which together with functional experiments and molecular dynamics simulations, reveal a mechanism for ion translocation and selectivity. Bulky hydrophobic residues from PomA prime PomA for clockwise rotation. We propose that a dynamic helical motif in PomA regulates the distance between PomA subunit cytoplasmic domains, stator unit activation, and torque transmission. Together, our study provides mechanistic insights for understanding ion selectivity and rotor incorporation of the stator unit of the bacterial flagellum.
History
DepositionNov 23, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16212.png

Downloads & links

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Map

FileDownload / File: emd_16212.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332.8 Å		0.83 Å/pix.
x 400 pix.
= 332.8 Å		0.83 Å/pix.
x 400 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-6.7509575 - 8.8597555
Average (Standard dev.)-0.0007832323 (±0.099316955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_16212_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16212_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : flagellar sodium-driven stator unit

EntireName: flagellar sodium-driven stator unit
Components
  • Complex: flagellar sodium-driven stator unit
    • Protein or peptide: Chemotaxis protein PomA
    • Protein or peptide: Flagellar motor protein,VaPomB
  • Protein or peptide: Chemotaxis protein PomA
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: flagellar sodium-driven stator unit

SupramoleculeName: flagellar sodium-driven stator unit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3
Source (natural)Organism: Vibrio alginolyticus (bacteria)

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Macromolecule #1: Chemotaxis protein PomA

MacromoleculeName: Chemotaxis protein PomA / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria)
Molecular weightTheoretical: 26.907633 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LATLLGLIGG FAFVIMAMVL GGSIGMFVDV TSILIVVGGS IFVVLMKFTM GQFFGATKIA GKAFMFKADE PEDLIAKIVE MADAARKGG FLALEEMEIN NTFMQKGIDL LVDGHDADVV RAALKKDIAL TDERHTQGTG VFRAFGDVAP AMGMIGTLVG L VAMLSNMD ...String:
LATLLGLIGG FAFVIMAMVL GGSIGMFVDV TSILIVVGGS IFVVLMKFTM GQFFGATKIA GKAFMFKADE PEDLIAKIVE MADAARKGG FLALEEMEIN NTFMQKGIDL LVDGHDADVV RAALKKDIAL TDERHTQGTG VFRAFGDVAP AMGMIGTLVG L VAMLSNMD DPKAIGPAMA VALLTTLYGA ILSNMVFFPI ADKLSLRRDQ ETLNRRLIMD GVLAIQDGQN PRVIDSYLKN YL NEGKRAL EID

UniProtKB: Chemotaxis protein PomA

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Macromolecule #2: Chemotaxis protein PomA

MacromoleculeName: Chemotaxis protein PomA / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria)
Molecular weightTheoretical: 27.038828 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 ALEI

UniProtKB: Chemotaxis protein PomA

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Macromolecule #3: Flagellar motor protein,VaPomB

MacromoleculeName: Flagellar motor protein,VaPomB / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria)
Molecular weightTheoretical: 5.704934 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PPPGLPLWMG TFADLMSLLM CFFVLLLSFS EMDVLKFKQI AGSMKFAFGV Q

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Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 12 / 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

Concentration16 mg/mL
BufferpH: 7.5 / Details: 300mM NaCl, 20mM HEPES 7.5, 0.002%LMNG
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 932963
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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