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- EMDB-0893: Detailed structures of the gliding machinery observed by ECT -

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Basic information

Entry
Database: EMDB / ID: EMD-0893
TitleDetailed structures of the gliding machinery observed by ECT
Map data
Sample
  • Cell: the jellyfish-like structure of Mycoplasma mobile
Biological speciesMycoplasma mobile (bacteria)
Methodelectron tomography / cryo EM
AuthorsKawamoto A / Kato T / Namba K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)25000013 Japan
CitationJournal: mBio / Year: 2019
Title: Refined Mechanism of Mycoplasma mobile Gliding Based on Structure, ATPase Activity, and Sialic Acid Binding of Machinery.
Authors: Miyuki S Nishikawa / Daisuke Nakane / Takuma Toyonaga / Akihiro Kawamoto / Takayuki Kato / Keiichi Namba / Makoto Miyata /
Abstract: , a fish pathogen, glides on solid surfaces by repeated catch, pull, and release of sialylated oligosaccharides by a unique mechanism based on ATP energy. The gliding machinery is composed of huge ..., a fish pathogen, glides on solid surfaces by repeated catch, pull, and release of sialylated oligosaccharides by a unique mechanism based on ATP energy. The gliding machinery is composed of huge surface proteins and an internal "jellyfish"-like structure. Here, we elucidated the detailed three-dimensional structures of the machinery by electron cryotomography. The internal "tentacle"-like structure hydrolyzed ATP, which was consistent with the fact that the paralogs of the α- and β-subunits of F-ATPase are at the tentacle structure. The electron microscopy suggested conformational changes of the tentacle structure depending on the presence of ATP analogs. The gliding machinery was isolated and showed that the binding activity to sialylated oligosaccharide was higher in the presence of ADP than in the presence of ATP. Based on these results, we proposed a model to explain the mechanism of gliding. The genus is made up of the smallest parasitic and sometimes commensal bacteria; , which causes human "walking pneumonia," is representative. More than ten species glide on host tissues by novel mechanisms, always in the direction of the distal side of the machinery. , the fastest species in the genus, catches, pulls, and releases sialylated oligosaccharides (SOs), the carbohydrate molecules also targeted by influenza viruses, by means of a specific receptor and using ATP hydrolysis for energy. Here, the architecture of the gliding machinery was visualized three dimensionally by electron cryotomography (ECT), and changes in the structure and binding activity coupled to ATP hydrolysis were discovered. Based on the results, a refined mechanism was proposed for this unique motility.
History
DepositionDec 9, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseJan 15, 2020-
UpdateJan 15, 2020-
Current statusJan 15, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Supplemental images

emd_0893.png

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Map

FileDownload / File: emd_0893.map.gz / Format: CCP4 / Size: 780 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 2 Å
Density
Minimum - Maximum-37739.074 - 27316.941
Average (Standard dev.)3941.98 (±899.8467)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin0086
Dimensions10241024195
Spacing10241024195
CellA: 2048.0 Å / B: 2048.0 Å / C: 390.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z10241024195
origin x/y/z0.0000.0000.000
length x/y/z2048.0002048.000390.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS0086
NC/NR/NS10241024195
D min/max/mean-37739.07427316.9413941.980

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Supplemental data

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Sample components

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Entire : the jellyfish-like structure of Mycoplasma mobile

EntireName: the jellyfish-like structure of Mycoplasma mobile
Components
  • Cell: the jellyfish-like structure of Mycoplasma mobile

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Supramolecule #1: the jellyfish-like structure of Mycoplasma mobile

SupramoleculeName: the jellyfish-like structure of Mycoplasma mobile / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Mycoplasma mobile (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.3
GridModel: Quantifoil R0.6/1 / Material: MOLYBDENUM / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: MP Biomedicals / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 78.0 K
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 10.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 37000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: IMOD (ver. 4.7) / Number images used: 1

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