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- PDB-6ysl: Structure of the flagellar MotAB stator complex from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 6ysl
TitleStructure of the flagellar MotAB stator complex from Bacillus subtilis
Components
  • Motility protein A
  • Motility protein B
KeywordsMOTOR PROTEIN / Stator Flagellar rotation ion driven motor
Function / homology
Function and homology information


archaeal or bacterial-type flagellum-dependent cell motility / bacterial-type flagellum-dependent swarming motility / monoatomic ion transport / chemotaxis / membrane => GO:0016020 / 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 superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile.
Similarity search - Domain/homology
Motility protein A / Motility protein B
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLea, S.M. / Deme, J.C. / Johnson, S.J.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust107929/Z/15/Z United Kingdom
Wellcome Trust100298/Z/12/Z United Kingdom
Wellcome Trust201536/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/M011984/1 United Kingdom
CitationJournal: Nat Microbiol / Year: 2020
Title: Structures of the stator complex that drives rotation of the bacterial flagellum.
Authors: Justin C Deme / Steven Johnson / Owen Vickery / Amy Aron / Holly Monkhouse / Thomas Griffiths / Rory Hennell James / Ben C Berks / James W Coulton / Phillip J Stansfeld / Susan M Lea /
Abstract: The bacterial flagellum is the prototypical protein nanomachine and comprises a rotating helical propeller attached to a membrane-embedded motor complex. The motor consists of a central rotor ...The bacterial flagellum is the prototypical protein nanomachine and comprises a rotating helical propeller attached to a membrane-embedded motor complex. The motor consists of a central rotor surrounded by stator units that couple ion flow across the cytoplasmic membrane to generate torque. Here, we present the structures of the stator complexes from Clostridium sporogenes, Bacillus subtilis and Vibrio mimicus, allowing interpretation of the extensive body of data on stator mechanism. The structures reveal an unexpected asymmetric AB subunit assembly where the five A subunits enclose the two B subunits. Comparison to structures of other ion-driven motors indicates that this AB architecture is fundamental to bacterial systems that couple energy from ion flow to generate mechanical work at a distance and suggests that such events involve rotation in the motor structures.
History
DepositionApr 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
G: Motility protein A
A: Motility protein B
B: Motility protein B
F: Motility protein A
E: Motility protein A
D: Motility protein A
C: Motility protein A


Theoretical massNumber of molelcules
Total (without water)205,9117
Polymers205,9117
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area25080 Å2
ΔGint-234 kcal/mol
Surface area58010 Å2
MethodPISA

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Components

#1: Protein
Motility protein A / / Chemotaxis protein MotA


Mass: 29370.221 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: motA, BSU13690 / Production host: Escherichia coli (E. coli) / References: UniProt: P28611
#2: Protein Motility protein B / / Chemotaxis protein MotB


Mass: 29529.768 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: motB, BSU13680 / Production host: Escherichia coli (E. coli) / References: UniProt: P28612

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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: MotA(5)B(2) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Bacillus subtilis (strain 168) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
1100 mMTris1
2150 mMNaClSodium chloride1
30.02 %LMNG1
SpecimenEmbedding 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 165000 X / Nominal defocus max: 0.3 nm / Nominal defocus min: 0.1 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_3126: / Classification: refinement
EM software
IDNameVersionCategory
1SIMPLE3particle selection
2EPUimage acquisition
4SIMPLE3CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10SIMPLE3initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1532430
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 122615 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00610322
ELECTRON MICROSCOPYf_angle_d1.14413971
ELECTRON MICROSCOPYf_dihedral_angle_d8.8056242
ELECTRON MICROSCOPYf_chiral_restr0.061698
ELECTRON MICROSCOPYf_plane_restr0.0081741

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