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- EMDB-10830: Structure of a protonation mimic of unplugged C. jejuni MotAB -

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Basic information

Entry
Database: EMDB / ID: EMD-10830
TitleStructure of a protonation mimic of unplugged C. jejuni MotAB
Map data
SampleStator unit MotAB(Delta41-60, D22N):
(Chemotaxis protein ...) x 2 / ligand
Function / homologyFlagellar motor protein MotA, conserved site / MotA/TolQ/ExbB proton channel / OmpA-like domain / Motility protein B, N-terminal domain / OmpA-like domain superfamily / integral component of membrane / Chemotaxis protein MotA, putative / Chemotaxis protein MotB, putative
Function and homology information
Biological speciesCampylobacter jejuni subsp. jejuni 81-176 (Campylobacter) / Campylobacter jejuni subsp. jejuni serotype O:23/36 (strain 81-176) (Campylobacter)
Methodsingle particle reconstruction / cryo EM / Resolution: 3 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.
Validation ReportPDB-ID: 6ykr

SummaryFull reportAbout validation report
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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  • Surface view with fitted model
  • Atomic models: PDB-6ykr
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10830.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-0.26193705 - 0.38684487
Average (Standard dev.)0.00043033095 (±0.010124373)
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-0.2620.3870.000

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Supplemental data

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Segmentation: #1

Fileemd_10830_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_10830_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_10830_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 MotAB(Delta41-60, D22N)

EntireName: Stator unit MotAB(Delta41-60, D22N)
Details: The stator unit consists of a dimer of MotB surrounded by a pentamer of MotA. Single mutation D22N simulates the protonated state of the channel. This stator unit is unplugged (deletion of ...Details: The stator unit consists of a dimer of MotB surrounded by a pentamer of MotA. Single mutation D22N simulates the protonated state of the channel. This stator unit is unplugged (deletion of aminoacids 41 to 60 of MotB).
Number of components: 4

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Component #1: protein, Stator unit MotAB(Delta41-60, D22N)

ProteinName: Stator unit MotAB(Delta41-60, D22N)
Details: The stator unit consists of a dimer of MotB surrounded by a pentamer of MotA. Single mutation D22N simulates the protonated state of the channel. This stator unit is unplugged (deletion of ...Details: The stator unit consists of a dimer of MotB surrounded by a pentamer of MotA. Single mutation D22N simulates the protonated state of the channel. This stator unit is unplugged (deletion of aminoacids 41 to 60 of MotB).
Recombinant expression: No
SourceSpecies: Campylobacter jejuni subsp. jejuni 81-176 (Campylobacter)
Source (engineered)Expression System: Escherichia coli (E. coli) / Strain: C43(DE3)

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Component #2: protein, Chemotaxis protein MotA, putative

ProteinName: Chemotaxis protein MotA, putative / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 28.195816 kDa
SourceSpecies: Campylobacter jejuni subsp. jejuni serotype O:23/36 (strain 81-176) (Campylobacter)
Strain: 81-176
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Chemotaxis protein MotB, putative

ProteinName: Chemotaxis protein MotB, putative / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 29.862643 kDa
SourceSpecies: Campylobacter jejuni subsp. jejuni serotype O:23/36 (strain 81-176) (Campylobacter)
Strain: 81-176
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: ligand, water

LigandName: water / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.68 mg/mL / pH: 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: 43.44 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: 456384
3D reconstructionSoftware: RELION / Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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