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- EMDB-3417: Structure of tetrameric MotA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-3417
TitleStructure of tetrameric MotA complex
Map dataReconstruction of Aquifex aeolicus stator protein, tetrameric MotA complex
Sample
  • Sample: Aquifex aeolicus MotA
  • Protein or peptide: Motility protein A
KeywordsFlagella motor / Stator / Single Particle analysis / Proton motive force
Function / homology
Function and homology information


bacterial-type flagellum-dependent swarming motility / proton transmembrane transport / chemotaxis / plasma membrane
Similarity search - Function
Flagellar motor protein MotA, conserved site / Flagellar motor protein motA family signature. / : / MotA/TolQ/ExbB proton channel / MotA/TolQ/ExbB proton channel family
Similarity search - Domain/homology
Biological speciesAquifex aeolicus (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsTakekawa N / Terahara N / Kato T / Gohara M / Mayanagi K / Hijikata A / Onoue Y / Kojima S / Shirai T / Namba K / Homma M
CitationJournal: Sci Rep / Year: 2016
Title: The tetrameric MotA complex as the core of the flagellar motor stator from hyperthermophilic bacterium.
Authors: Norihiro Takekawa / Naoya Terahara / Takayuki Kato / Mizuki Gohara / Kouta Mayanagi / Atsushi Hijikata / Yasuhiro Onoue / Seiji Kojima / Tsuyoshi Shirai / Keiichi Namba / Michio Homma /
Abstract: Rotation of bacterial flagellar motor is driven by the interaction between the stator and rotor, and the driving energy is supplied by ion influx through the stator channel. The stator is composed of ...Rotation of bacterial flagellar motor is driven by the interaction between the stator and rotor, and the driving energy is supplied by ion influx through the stator channel. The stator is composed of the MotA and MotB proteins, which form a hetero-hexameric complex with a stoichiometry of four MotA and two MotB molecules. MotA and MotB are four- and single-transmembrane proteins, respectively. To generate torque, the MotA/MotB stator unit changes its conformation in response to the ion influx, and interacts with the rotor protein FliG. Here, we overproduced and purified MotA of the hyperthermophilic bacterium Aquifex aeolicus. A chemical crosslinking experiment revealed that MotA formed a multimeric complex, most likely a tetramer. The three-dimensional structure of the purified MotA, reconstructed by electron microscopy single particle imaging, consisted of a slightly elongated globular domain and a pair of arch-like domains with spiky projections, likely to correspond to the transmembrane and cytoplasmic domains, respectively. We show that MotA molecules can form a stable tetrameric complex without MotB, and for the first time, demonstrate the cytoplasmic structure of the stator.
History
DepositionApr 27, 2016-
Header (metadata) releaseMay 18, 2016-
Map releaseAug 2, 2017-
UpdateAug 2, 2017-
Current statusAug 2, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3417.png

emd_3417_1.png

Downloads & links

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Map

FileDownload / File: emd_3417.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Aquifex aeolicus stator protein, tetrameric MotA complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 64 pix.
= 179.2 Å		2.8 Å/pix.
x 64 pix.
= 179.2 Å		2.8 Å/pix.
x 64 pix.
= 179.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-3.35296297 - 3.4676733
Average (Standard dev.)0.01830916 (±0.3995882)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-32-32-32
Dimensions646464
Spacing646464
CellA=B=C: 179.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z179.200179.200179.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
D min/max/mean-3.3533.4680.018

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Supplemental data

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Sample components

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Entire : Aquifex aeolicus MotA

EntireName: Aquifex aeolicus MotA
Components
  • Sample: Aquifex aeolicus MotA
  • Protein or peptide: Motility protein A

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Supramolecule #1000: Aquifex aeolicus MotA

SupramoleculeName: Aquifex aeolicus MotA / type: sample / ID: 1000 / Oligomeric state: tetramer / Number unique components: 1
Molecular weightTheoretical: 109 KDa

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Macromolecule #1: Motility protein A

MacromoleculeName: Motility protein A / type: protein_or_peptide / ID: 1 / Name.synonym: Chemotaxis protein MotA / Number of copies: 4 / Oligomeric state: Tetramer / Recombinant expression: Yes
Source (natural)Organism: Aquifex aeolicus (bacteria) / Strain: VF5
Molecular weightTheoretical: 109 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21-CodonPlus(DE3)-RIPL / Recombinant plasmid: pColdI
SequenceUniProtKB: Motility protein A

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 8 / Details: 50 mM Tris-HCl, 200 mM NaCl, 0.02% DMNG
StainingType: NEGATIVE / Details: 2% w/v uranyl acetate
GridDetails: 200 mesh copper grid with continuous carbon suport, glow discharged
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureMin: 85.5 K / Max: 85.7 K / Average: 85.5 K
Specialist opticsEnergy filter - Name: Omega Filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateNov 16, 2015
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Number real images: 50 / Average electron dose: 2.8 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 107140 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.135 µm / Nominal magnification: 80000
Sample stageSpecimen holder: Nitrogen cooled / Specimen holder model: JEOL 3200FSC CRYOHOLDER

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Relion-1.4 / Number images used: 5419

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