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- EMDB-10901: Vibrio mimicus PomA(5)B(2) complex -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-10901
TitleVibrio mimicus PomA(5)B(2) complex
Map dataPost Processed Vibrio mimicus PomAB complex volume
Sample
  • Complex: PomA(5)B(2)
    • Protein or peptide: PomA
    • Protein or peptide: PomB
Function / homology
Function and homology information


bacterial-type flagellum-dependent swarming motility / 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 PomA / Flagellar motor protein
Similarity search - Component
Biological speciesClostridium sporogenes (bacteria) / Vibrio mimicus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsLea SM / Deme JC / Johnson S
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 26, 2021-
Current statusMay 26, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10901.png

Downloads & links

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Map

FileDownload / File: emd_10901.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost Processed Vibrio mimicus PomAB complex volume
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 288 pix.
= 236.736 Å		0.82 Å/pix.
x 288 pix.
= 236.736 Å		0.82 Å/pix.
x 288 pix.
= 236.736 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: 0.0155 / Movie #1: 0.012
Minimum - Maximum-0.032297056 - 0.054492336
Average (Standard dev.)1.3986626e-05 (±0.0019340492)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 236.73601 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8220.8220.822
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z236.736236.736236.736
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0320.0540.000

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Supplemental data

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Mask #1

Fileemd_10901_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 Vibrio mimicus PomAB complex volume

Fileemd_10901_additional_1.map
Annotationrelion local resolution Vibrio mimicus PomAB complex volume
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: refinement volume

Fileemd_10901_additional_2.map
Annotationrefinement volume
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: half map 1

Fileemd_10901_additional_3.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: half map 2

Fileemd_10901_additional_4.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 : PomA(5)B(2)

EntireName: PomA(5)B(2)
Components
  • Complex: PomA(5)B(2)
    • Protein or peptide: PomA
    • Protein or peptide: PomB

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

SupramoleculeName: PomA(5)B(2) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium sporogenes (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: PomA

MacromoleculeName: PomA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio mimicus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDLATLIGLI GGLAFVIMAM VLGGSLMMFV DVVSILIVVG GSVFVVLMKF TMGQFFGAGK IASKAFMFK ADEPEDLIAK IVEMADAARK GGFLALEEME IPNPFMQKGI DLLVDGHDAD V VRATLQKD IALTDERHSK GTQVFRAFGD VAPAMGMIST LVGLVAMLSN ...String:
MDLATLIGLI GGLAFVIMAM VLGGSLMMFV DVVSILIVVG GSVFVVLMKF TMGQFFGAGK IASKAFMFK ADEPEDLIAK IVEMADAARK GGFLALEEME IPNPFMQKGI DLLVDGHDAD V VRATLQKD IALTDERHSK GTQVFRAFGD VAPAMGMIST LVGLVAMLSN MDDPKSIGPA MA VALLTTL YGAVLSNMIF FPIADKLALR RDQETLNRRL IMDGVLAIQD GQNPRVIDSY LKN YLNASK RALDVDKE

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Macromolecule #2: PomB

MacromoleculeName: PomB / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio mimicus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDDEQQCKCP PPGLPAWLGT FADLMSLLMC FFVLLLSFSE MDVLKFKQIA GSMKFAFGVQ NRLEVKDIP KGTSIIAQEF RPGRPEPTPI DVIMQQTIDI TQQTLDFQEG DSDRAGGNQR D SGKLTGGQ SAESSTQDNQ NTQSEMQQQQ AKAMSEQMET VAESIKKALS ...String:
MDDEQQCKCP PPGLPAWLGT FADLMSLLMC FFVLLLSFSE MDVLKFKQIA GSMKFAFGVQ NRLEVKDIP KGTSIIAQEF RPGRPEPTPI DVIMQQTIDI TQQTLDFQEG DSDRAGGNQR D SGKLTGGQ SAESSTQDNQ NTQSEMQQQQ AKAMSEQMET VAESIKKALS REIEQGAIEV EN LGQQIDI RIREKGAFPE GSAFLQPKFR PLVRQIADLV KDIPGKVRVT GHTDNQKLDS ELY RSNWDL SAQRAVSVAQ EMEKVKGFDH QRLQVRGMAD TQPLGPNDTE AQRALNRRVE ISIL QGDPL YSDEVPSLGA PANQ

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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: 2383022
CTF correctionSoftware - Name: SIMPLE (ver. 3.0)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 244654
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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