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- PDB-8bri: VaPomAB MSP1D1 nanodisc -

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Basic information

Entry
Database: PDB / ID: 8bri
TitleVaPomAB MSP1D1 nanodisc
Components
  • Chemotaxis protein PomA
  • Flagellar motor protein
KeywordsMOTOR PROTEIN / Flagellar sodium-driven stator unit
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
Flagellar motor protein / Chemotaxis protein PomA
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHu, H. / Taylor, N.M.I.
Funding support Denmark, 3items
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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.0Jun 14, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Jun 14, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 14, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
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Revision 1.0Jun 14, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Jun 14, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jun 14, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 14, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Jun 14, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 9, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chemotaxis protein PomA
B: Chemotaxis protein PomA
C: Chemotaxis protein PomA
D: Chemotaxis protein PomA
E: Chemotaxis protein PomA
F: Flagellar motor protein
G: Flagellar motor protein


Theoretical massNumber of molelcules
Total (without water)207,5907
Polymers207,5907
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Chemotaxis protein PomA


Mass: 27283.031 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Gene: pomA / Production host: Escherichia coli (E. coli) / References: UniProt: O06873
#2: Protein Flagellar motor protein


Mass: 35587.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Gene: N646_2843 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2I3CFY6
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: flagellar sodium-driven stator unit / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Vibrio alginolyticus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 300mM NaCl, 20mM HEPES 7.5, 0.002%LMNG
SpecimenConc.: 16 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 38 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.9 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Num. of particles: 66296 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00510061
ELECTRON MICROSCOPYf_angle_d1.2913549

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