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- EMDB-3417: Structure of tetrameric MotA complex -

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Basic information

Entry
Database: EMDB / ID: 3417
TitleStructure of tetrameric MotA complex
KeywordsFlagella motor / Stator / Single Particle analysis / Proton motive force
SampleAquifex aeolicus MotA
SourceAquifex aeolicus / bacteria
Map dataReconstruction of Aquifex aeolicus stator protein, tetrameric MotA complex
Methodsingle particle reconstruction, at 25 Å resolution
AuthorsTakekawa N / Terahara N / Kato T / Gohara M / Mayanagi K / Hijikata A / Onoue Y / Kojima S / Shirai T / Namba K / Homma M
CitationSci Rep, 2016, 6, 31526-31526

Sci Rep, 2016, 6, 31526-31526 StrPapers
The tetrameric MotA complex as the core of the flagellar motor stator from hyperthermophilic bacterium.
Norihiro Takekawa / Naoya Terahara / Takayuki Kato / Mizuki Gohara / Kouta Mayanagi / Atsushi Hijikata / Yasuhiro Onoue / Seiji Kojima / Tsuyoshi Shirai / Keiichi Namba / Michio Homma

DateDeposition: Apr 27, 2016 / Header (metadata) release: May 18, 2016 / Map release: Aug 2, 2017 / Last update: Aug 2, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_3417.map.gz (map file in CCP4 format, 1025 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
2.8 Å/pix.
= 179.2 Å
64 pix
2.8 Å/pix.
= 179.2 Å
64 pix
2.8 Å/pix.
= 179.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.8 Å
Density
Contour Level:1 (by author), 1 (movie #1):
Minimum - Maximum-3.35296297 - 3.4676733
Average (Standard dev.)0.01830916 (0.3995882)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin-32-32-32
Limit313131
Spacing646464
CellA=B=C: 179.2 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
NX/NY/NZ
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 / Number of components: 1 / Oligomeric State: tetramer
MassTheoretical: 109 kDa

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Component #1: protein, Motility protein A

ProteinName: Motility protein A / a.k.a: Chemotaxis protein MotA / Oligomeric Details: Tetramer / Recombinant expression: Yes / Number of Copies: 4
MassTheoretical: 109 kDa
SourceSpecies: Aquifex aeolicus / bacteria / Strain: VF5
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pColdI / Strain: BL21-CodonPlus(DE3)-RIPL
External referencesUniProt: UniProt: O67122

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.1 mg/ml / Buffer solution: 50 mM Tris-HCl, 200 mM NaCl, 0.02% DMNG / pH: 8
Support film200 mesh copper grid with continuous carbon suport, glow discharged
Staining2% w/v uranyl acetate
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC / Date: Nov 16, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2.8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 80000 X (nominal), 107140 X (calibrated) / Cs: 4.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 1135 - 2200 nm / Energy filter: Omega Filter / Energy window: 0-20 eV
Specimen HolderHolder: Nitrogen cooled / Model: JEOL 3200FSC CRYOHOLDER / Temperature: 85.5 K ( 85.5 - 85.7 K)
CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 50

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 5419
3D reconstructionSoftware: Relion-1.4 / Resolution: 25 Å / Resolution method: FSC 0.143

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