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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
Sample
  • Complex: Stator unit MotAB(Delta41-60, D22N)
    • Protein or peptide: Chemotaxis protein MotA, putative
    • Protein or peptide: Chemotaxis protein MotB, putative
  • Ligand: water
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 superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile.
Similarity search - Domain/homology
Chemotaxis protein MotA, putative / Chemotaxis protein MotB, putative
Similarity search - Component
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: 3.0 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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  • Surface view with fitted model
  • Atomic models: PDB-6ykr
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10830.png

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)
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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Mask #1

Fileemd_10830_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10830_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_10830_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Stator unit MotAB(Delta41-60, D22N)

EntireName: Stator unit MotAB(Delta41-60, D22N)
Components
  • Complex: Stator unit MotAB(Delta41-60, D22N)
    • Protein or peptide: Chemotaxis protein MotA, putative
    • Protein or peptide: Chemotaxis protein MotB, putative
  • Ligand: water

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

SupramoleculeName: Stator unit MotAB(Delta41-60, D22N) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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).
Source (natural)Organism: Campylobacter jejuni subsp. jejuni 81-176 (Campylobacter)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: C43(DE3)

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Macromolecule #1: Chemotaxis protein MotA, putative

MacromoleculeName: Chemotaxis protein MotA, putative / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Campylobacter jejuni subsp. jejuni serotype O:23/36 (strain 81-176) (Campylobacter)
Strain: 81-176
Molecular weightTheoretical: 28.195816 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDLSTILGMV LAVTSISVGD ILEGGNPLHV IHLSSFLIVM PTAAFCAMTS THKKIVKAAY KELKVVFKGS GVNLPERIAQ LIEFAIIAR RDGLLALESR TNEIENEFLK NAMMMLVDGK SFEEIHESME IQTEQLEEHY KECAEYWIVF GETCPTMGLV G AVFGLILA ...String:
MDLSTILGMV LAVTSISVGD ILEGGNPLHV IHLSSFLIVM PTAAFCAMTS THKKIVKAAY KELKVVFKGS GVNLPERIAQ LIEFAIIAR RDGLLALESR TNEIENEFLK NAMMMLVDGK SFEEIHESME IQTEQLEEHY KECAEYWIVF GETCPTMGLV G AVFGLILA LKLLDNPQAM AAGISGAFTA TVTGIFGAYA LFAPWGKKLK ANGMDLVKEQ IVITEAIKGI AEGANPRDLE AK LFNFLSH DDPRISQFDK G

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Macromolecule #2: Chemotaxis protein MotB, putative

MacromoleculeName: Chemotaxis protein MotB, putative / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Campylobacter jejuni subsp. jejuni serotype O:23/36 (strain 81-176) (Campylobacter)
Strain: 81-176
Molecular weightTheoretical: 29.862643 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAKKHKCPEC PAGEKWAVPY ANFLSLLLAL FIALWAISKT TQTVKEESKT QEKYKGAAKE ESDELKSLKQ MTMTQQETIK RLQAALDQS DNQVALNLPS KVEFERGSAQ IVSADIQDYL KRMAELTTYL PPQAKIEIRG YTDNSDSIIR SYELAYQRAE N VLKYFIEG ...String:
MAKKHKCPEC PAGEKWAVPY ANFLSLLLAL FIALWAISKT TQTVKEESKT QEKYKGAAKE ESDELKSLKQ MTMTQQETIK RLQAALDQS DNQVALNLPS KVEFERGSAQ IVSADIQDYL KRMAELTTYL PPQAKIEIRG YTDNSDSIIR SYELAYQRAE N VLKYFIEG GANLKNISIK SYGLNNPING NPQALENNRV EIYFKVDTAD TSTQKSVLEL INKIGTKAPG TLEVLFQGPG GS GSAWSHP QFEKGGGSGG GSGGSAWSHP QFEK

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 6 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

Concentration0.68 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/1 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 43.44 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 456384
FSC plot (resolution estimation)

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