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- EMDB-31520: Negative stain map of chained F1-like ATPase complex of Mycoplasm... -

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Basic information

Entry
Database: EMDB / ID: EMD-31520
TitleNegative stain map of chained F1-like ATPase complex of Mycoplasma mobile
Map data
Sample
  • Complex: Negative stain map of chained F1-like ATPase complex of MYcoplasma mobile
Biological speciesMycoplasma mobile (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 29.7 Å
AuthorsToyonaga T / Miyata M
Funding support Japan, 1 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)24117002 Japan
Citation
Journal: mBio / Year: 2021
Title: Chained Structure of Dimeric F-like ATPase in Mycoplasma mobile Gliding Machinery.
Authors: Takuma Toyonaga / Takayuki Kato / Akihiro Kawamoto / Noriyuki Kodera / Tasuku Hamaguchi / Yuhei O Tahara / Toshio Ando / Keiichi Namba / Makoto Miyata /
Abstract: Mycoplasma mobile, a fish pathogen, exhibits gliding motility using ATP hydrolysis on solid surfaces, including animal cells. The gliding machinery can be divided into surface and internal structures. ...Mycoplasma mobile, a fish pathogen, exhibits gliding motility using ATP hydrolysis on solid surfaces, including animal cells. The gliding machinery can be divided into surface and internal structures. The internal structure of the motor is composed of 28 so-called "chains" that are each composed of 17 repeating protein units called "particles." These proteins include homologs of the catalytic α and β subunits of F-ATPase. In this study, we isolated the particles and determined their structures using negative-staining electron microscopy and high-speed atomic force microscopy. The isolated particles were composed of five proteins, MMOB1660 (α-subunit homolog), -1670 (β-subunit homolog), -1630, -1620, and -4530, and showed ATP hydrolyzing activity. The two-dimensional (2D) structure, with dimensions of 35 and 26 nm, showed a dimer of hexameric ring approximately 12 nm in diameter, resembling F-ATPase catalytic (αβ). We isolated the F-like ATPase unit, which is composed of MMOB1660, -1670, and -1630. Furthermore, we isolated the chain and analyzed the three-dimensional (3D) structure, showing that dimers of mushroom-like structures resembling F-ATPase were connected and aligned along the dimer axis at 31-nm intervals. An atomic model of F-ATPase catalytic (αβ) from PS3 was successfully fitted to each hexameric ring of the mushroom-like structure. These results suggest that the motor for gliding shares an evolutionary origin with F-ATPase. Based on the obtained structure, we propose possible force transmission processes in the gliding mechanism. FF-ATPase, a rotary ATPase, is widespread in the membranes of mitochondria, chloroplasts, and bacteria and converts ATP energy with a proton motive force across the membrane by its physical rotation. Homologous protein complexes play roles in ion and protein transport. Mycoplasma mobile, a pathogenic bacterium, was recently suggested to have a special motility system evolutionarily derived from F-ATPase. The present study isolated the protein complex from cells and supported this conclusion by clarifying the detailed structures containing common and novel features as F-ATPase relatives.
#1: Journal: mBio / Year: 2021
Title: Chained structure of dimeric F1-like ATPase in Mycoplasma mobile gliding machinery
Authors: Toyonaga T / Kato T / Kawamoto A / Kodera K / Hamaguchi T / Tahara YO / Ando T / Namba K / Miyata M
History
DepositionJul 13, 2021-
Header (metadata) releaseAug 11, 2021-
Map releaseAug 11, 2021-
UpdateSep 15, 2021-
Current statusSep 15, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31520.png

Downloads & links

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Map

FileDownload / File: emd_31520.map.gz / Format: CCP4 / Size: 10 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 5.16 Å
Density
Contour LevelBy AUTHOR: 0.026 / Movie #1: 0.026
Minimum - Maximum-0.05757904 - 0.08018699
Average (Standard dev.)-0.0008774695 (±0.0074919374)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions138138138
Spacing138138138
CellA=B=C: 712.07996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.165.165.16
M x/y/z138138138
origin x/y/z0.0000.0000.000
length x/y/z712.080712.080712.080
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS138138138
D min/max/mean-0.0580.080-0.001

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Supplemental data

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Sample components

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Entire : Negative stain map of chained F1-like ATPase complex of MYcoplasm...

EntireName: Negative stain map of chained F1-like ATPase complex of MYcoplasma mobile
Components
  • Complex: Negative stain map of chained F1-like ATPase complex of MYcoplasma mobile

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Supramolecule #1: Negative stain map of chained F1-like ATPase complex of MYcoplasm...

SupramoleculeName: Negative stain map of chained F1-like ATPase complex of MYcoplasma mobile
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mycoplasma mobile (bacteria)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.3
StainingType: NEGATIVE / Material: Uranyl Acetate

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Electron microscopy

MicroscopeJEOL 1010
Image recordingFilm or detector model: OTHER / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 80 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Particle selectionNumber selected: 2127
Final reconstructionResolution.type: BY AUTHOR / Resolution: 29.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 1907
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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