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- EMDB-10899: Structure of the flagellar MotAB stator complex from Bacillus subtilis -

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Basic information

Entry
Database: EMDB / ID: EMD-10899
TitleStructure of the flagellar MotAB stator complex from Bacillus subtilis
Map dataBacillus subtilis MotAB complex volume post processed
Sample
  • Complex: MotA(5)B(2)
    • Protein or peptide: Motility protein A
    • Protein or peptide: Motility protein B
KeywordsStator Flagellar rotation ion driven motor / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum stator complex / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum-dependent cell motility / proton transmembrane transport / chemotaxis / plasma membrane
Similarity search - Function
Motility protein A, N-terminal / Motility protein A N-terminal / 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 / : ...Motility protein A, N-terminal / Motility protein A N-terminal / 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
Motility protein A / Motility protein B
Similarity search - Component
Biological speciesBacillus subtilis (strain 168) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLea SM / Deme JC
Funding support United Kingdom, 4 items
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, 2020-
Header (metadata) releaseAug 12, 2020-
Map releaseAug 12, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ysl
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10899.png

Downloads & links

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Map

FileDownload / File: emd_10899.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacillus subtilis MotAB complex volume post processed
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 210.432 Å		0.82 Å/pix.
x 256 pix.
= 210.432 Å		0.82 Å/pix.
x 256 pix.
= 210.432 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.054929722 - 0.09134688
Average (Standard dev.)0.000040963834 (±0.0030038182)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 210.432 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8220.8220.822
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z210.432210.432210.432
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0550.0910.000

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Supplemental data

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Mask #1

Fileemd_10899_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Bacillus subtilis MotAB complex volume relion local resolution...

Fileemd_10899_additional_1.map
AnnotationBacillus subtilis MotAB complex volume relion local resolution filtered
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Bacillus subtilis MotAB complex volume calculated from subset...

Fileemd_10899_additional_2.map
AnnotationBacillus subtilis MotAB complex volume calculated from subset of particles with added fluo-OM
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Bacillus subtilis MotAB complex volume refinement volume

Fileemd_10899_additional_3.map
AnnotationBacillus subtilis MotAB complex volume refinement volume
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Bacillus subtilis MotAB complex volume half map 1

Fileemd_10899_half_map_1.map
AnnotationBacillus subtilis MotAB complex volume half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Bacillus subtilis MotAB complex volume half map 2

Fileemd_10899_half_map_2.map
AnnotationBacillus subtilis MotAB complex volume half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MotA(5)B(2)

EntireName: MotA(5)B(2)
Components
  • Complex: MotA(5)B(2)
    • Protein or peptide: Motility protein A
    • Protein or peptide: Motility protein B

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Supramolecule #1: MotA(5)B(2)

SupramoleculeName: MotA(5)B(2) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus subtilis (strain 168) (bacteria)

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Macromolecule #1: Motility protein A

MacromoleculeName: Motility protein A / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (strain 168) (bacteria)
Molecular weightTheoretical: 29.370221 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDKTSLIGII LAFVALSVGM VLKGVSFSAL ANPAAILIII AGTISAVVIA FPTKEIKKVP TLFRVLFKEN KQLTIEELIP MFSEWAQLA RREGLLALEA SIEDVDDAFL KNGLSMAVDG QSAEFIRDIM TEEVEAMEDR HQAGAAIFTQ AGTYAPTLGV L GAVIGLIA ...String:
MDKTSLIGII LAFVALSVGM VLKGVSFSAL ANPAAILIII AGTISAVVIA FPTKEIKKVP TLFRVLFKEN KQLTIEELIP MFSEWAQLA RREGLLALEA SIEDVDDAFL KNGLSMAVDG QSAEFIRDIM TEEVEAMEDR HQAGAAIFTQ AGTYAPTLGV L GAVIGLIA ALSHMDNTDE LGHAISAAFV ATLLGIFTGY VLWHPFANKL KRKSKQEVKL REVMIEGVLS VLEGQAPKVI EQ KLLMYLP AKDRLKFAEQ GEAQNGEKKE EEA

UniProtKB: Motility protein A

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Macromolecule #2: Motility protein B

MacromoleculeName: Motility protein B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (strain 168) (bacteria)
Molecular weightTheoretical: 29.529768 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MARKKKKKHE DEHVDESWLV PYADILTLLL ALFIVLYASS SIDAAKFQML SKSFNEVFTG GTGVLDYSSV TPPENESDGI DEVKKEKEE KEKNKKEKEK AADQEELENV KSQVEKFIKD KKLEHQLETK MTSEGLLITI KDSIFFDSGK ATIRKEDVPL A KEISNLLV ...String:
MARKKKKKHE DEHVDESWLV PYADILTLLL ALFIVLYASS SIDAAKFQML SKSFNEVFTG GTGVLDYSSV TPPENESDGI DEVKKEKEE KEKNKKEKEK AADQEELENV KSQVEKFIKD KKLEHQLETK MTSEGLLITI KDSIFFDSGK ATIRKEDVPL A KEISNLLV INPPRNIIIS GHTDNMPIKN SEFQSNWHLS VMRAVNFMGL LIENPKLDAK VFSAKGYGEY KPVASNKTAE GR SKNRRVE VLILPRGAAE TNEK

UniProtKB: Motility protein B

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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: 7.5
Component:
ConcentrationName
100.0 mMTris
150.0 mMNaCl
0.02 %LMNG
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.0003 µm / Nominal defocus min: 0.0001 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1532430
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 122615
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SIMPLE (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

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

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