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- EMDB-10895: Structure of the flagellar MotAB stator complex from Clostridium ... -

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Basic information

Entry
Database: EMDB / ID: EMD-10895
TitleStructure of the flagellar MotAB stator complex from Clostridium sporogenes
Map datapost processed volume MotAB complex clostridium sporogenes
Sample
  • Complex: MotAB
    • Protein or peptide: Chemotaxis motB protein
    • Protein or peptide: Chemotaxis MotA protein
KeywordsStator Flagellar rotation ion driven motor / MOTOR PROTEIN
Function / homology
Function and homology information


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 profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain
Similarity search - Domain/homology
Chemotaxis protein MotB / Chemotaxis MotA protein
Similarity search - Component
Biological speciesClostridium sporogenes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6ysf
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10895.png

Downloads & links

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Map

FileDownload / File: emd_10895.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpost processed volume MotAB complex clostridium sporogenes
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: 0.0228 / Movie #1: 0.017
Minimum - Maximum-0.06770912 - 0.10926956
Average (Standard dev.)0.000025380956 (±0.0032657946)
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-0.0680.1090.000

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Supplemental data

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Mask #1

Fileemd_10895_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Relion Local Resolution filtered volume MotAB clostridium sporogenes

Fileemd_10895_additional_1.map
AnnotationRelion Local Resolution filtered volume MotAB clostridium sporogenes
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Refinement volume MotAB clostridium sporogenes

Fileemd_10895_additional_2.map
AnnotationRefinement volume MotAB clostridium sporogenes
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_10895_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_10895_half_map_2.map
Annotationhalf 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 : MotAB

EntireName: MotAB
Components
  • Complex: MotAB
    • Protein or peptide: Chemotaxis motB protein
    • Protein or peptide: Chemotaxis MotA protein

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Supramolecule #1: MotAB

SupramoleculeName: MotAB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium sporogenes (bacteria)

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Macromolecule #1: Chemotaxis motB protein

MacromoleculeName: Chemotaxis motB protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Clostridium sporogenes (bacteria)
Molecular weightTheoretical: 27.948547 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MARRNKKGGG GDEIRGDEWL ATFSDTITLL LTFFILLYSF SSVDAQKFQQ VASAMQVAMT GQSGNTIVDY NLKNGDVPLV GETTKLGRE TGSDAKSDSK EVYNEVNKFV DKNNLKSSVE VKEDGRGVII QLRDNVLFEI GRADIKPQSK QIMDKINGLI A TLPNEVIV ...String:
MARRNKKGGG GDEIRGDEWL ATFSDTITLL LTFFILLYSF SSVDAQKFQQ VASAMQVAMT GQSGNTIVDY NLKNGDVPLV GETTKLGRE TGSDAKSDSK EVYNEVNKFV DKNNLKSSVE VKEDGRGVII QLRDNVLFEI GRADIKPQSK QIMDKINGLI A TLPNEVIV EGHTDNVPIK NEVYGSNWEL STARAVNVLR YFVETKKQNP VRFTAAGYGE YRPIAQNNSD VNKAKNRRVN IV IVSKEKE SSKK

UniProtKB: Chemotaxis protein MotB

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Macromolecule #2: Chemotaxis MotA protein

MacromoleculeName: Chemotaxis MotA protein / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Clostridium sporogenes (bacteria)
Molecular weightTheoretical: 29.613506 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKRDILTPI GFVLCFGLVL WGMASGGSNL KVFWDVASVF ITIGGSMAAM LITYPMDEFK RLLIVIRQTF KDNGMSNIDV IQNFVDLSR KARREGLLSL EDAINNLTDD YMKKGLRMVV DGIEPETIRE IMELEIDEME KRHKSGADML KTWGGYAPAF G MVGTLIGL ...String:
MKKRDILTPI GFVLCFGLVL WGMASGGSNL KVFWDVASVF ITIGGSMAAM LITYPMDEFK RLLIVIRQTF KDNGMSNIDV IQNFVDLSR KARREGLLSL EDAINNLTDD YMKKGLRMVV DGIEPETIRE IMELEIDEME KRHKSGADML KTWGGYAPAF G MVGTLIGL IQMLANLTDS STIASGMGKA LITTFYGSLM ANAVFNPMGA NLMFKSGVEA TTREMVLEGV LAIQSGVNPR IM EEKLVSY LSPPERQAYS KVQVSGEGAA QNG

UniProtKB: Chemotaxis MotA protein

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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
20.0 mMHEPES
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: 1998900
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 314230
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-6ysf:
Structure of the flagellar MotAB stator complex from Clostridium sporogenes

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