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- EMDB-10832: Structure of V. alginolyticus PomAB -

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Basic information

Entry
Database: EMDB / ID: EMD-10832
TitleStructure of V. alginolyticus PomAB
Map data
SampleStator unit PomAB:
PomA / PomB
Function / homologyMotA/TolQ/ExbB proton channel / OmpA-like domain / Putative MotA/TolQ/ExbB family protein / Motility protein B, N-terminal domain / OmpA-like domain superfamily / protein transport / integral component of membrane / Flagellar motor protein MotB / Flagellar motor protein MotA
Function and homology information
Biological speciesVibrio alginolyticus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.45 Å
AuthorsSantiveri M / Roa-Eguiara A / Taylor NMI
Funding support Denmark, 2 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
Danish Council for Independent Research8123-00002B Denmark
CitationJournal: Cell / Year: 2020
Title: Structure and Function of Stator Units of the Bacterial Flagellar Motor.
Authors: Mònica Santiveri / Aritz Roa-Eguiara / Caroline Kühne / Navish Wadhwa / Haidai Hu / Howard C Berg / Marc Erhardt / Nicholas M I Taylor /
Abstract: Many bacteria use the flagellum for locomotion and chemotaxis. Its bidirectional rotation is driven by a membrane-embedded motor, which uses energy from the transmembrane ion gradient to generate ...Many bacteria use the flagellum for locomotion and chemotaxis. Its bidirectional rotation is driven by a membrane-embedded motor, which uses energy from the transmembrane ion gradient to generate torque at the interface between stator units and rotor. The structural organization of the stator unit (MotAB), its conformational changes upon ion transport, and how these changes power rotation of the flagellum remain unknown. Here, we present ~3 Å-resolution cryoelectron microscopy reconstructions of the stator unit in different functional states. We show that the stator unit consists of a dimer of MotB surrounded by a pentamer of MotA. Combining structural data with mutagenesis and functional studies, we identify key residues involved in torque generation and present a detailed mechanistic model for motor function and switching of rotational direction.
History
DepositionApr 6, 2020-
Header (metadata) releaseSep 30, 2020-
Map releaseSep 30, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10832.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.992 Å
0.83 Å/pix.
x 256 pix.
= 212.992 Å
0.83 Å/pix.
x 256 pix.
= 212.992 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.3890095 - 0.45341346
Average (Standard dev.)0.00035089525 (±0.014479909)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.992 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8320.8320.832
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z212.992212.992212.992
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.3890.4530.000

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Supplemental data

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Segmentation: #1

Fileemd_10832_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_10832_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_10832_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Stator unit PomAB

EntireName: Stator unit PomAB
Details: The stator unit consists of a dimer of PomB surrounded by a pentamer of PomA
Number of components: 3

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Component #1: protein, Stator unit PomAB

ProteinName: Stator unit PomAB
Details: The stator unit consists of a dimer of PomB surrounded by a pentamer of PomA
Recombinant expression: No
SourceSpecies: Vibrio alginolyticus (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli) / Strain: C43(DE3)

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Component #2: protein, PomA

ProteinName: PomA / Recombinant expression: No
SourceSpecies: Vibrio alginolyticus (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, PomB

ProteinName: PomB / Recombinant expression: No
SourceSpecies: Vibrio alginolyticus (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 42.82 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 91076
3D reconstructionSoftware: RELION / Resolution: 6.45 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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