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- EMDB-26216: Methylococcus capsulatus methane monooxygenase hydroxylase (MMOH)... -

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Basic information

Entry
Database: EMDB / ID: EMD-26216
TitleMethylococcus capsulatus methane monooxygenase hydroxylase (MMOH) using the plasma-jet treated grid
Map data
Sample
  • Complex: The ternary complex of two subunits of MMOH_alpha, MMOH_beta, and MMOH_gamma
Biological speciesMethylococcus capsulatus str. Texas = ATCC 19069 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsAhn E / Kim B / Cho US
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)111465 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)250329 United States
CitationJournal: J Biol Chem / Year: 2022
Title: Development of an atmospheric plasma jet device for versatile treatment of electron microscope sample grids.
Authors: Eungjin Ahn / Tianyu Tang / Byungchul Kim / Hae June Lee / Uhn-Soo Cho /
Abstract: Atmospheric-pressure plasmas have been widely applied for surface modification and biomedical treatment because of their ability to generate highly reactive radicals and charged particles. In ...Atmospheric-pressure plasmas have been widely applied for surface modification and biomedical treatment because of their ability to generate highly reactive radicals and charged particles. In negative-stain electron microscopy (Neg-EM) and cryogenic electron microscopy (cryo-EM), plasmas have been used to generate hydrophilic surfaces and eliminate surface contaminants to embed specimens onto grids. In addition, plasma treatment is a prerequisite for negative-stain and Quantifoil grids, whose surfaces are coated with hydrophobic amorphous carbon. Although the conventional glow discharge system has been used successfully in this purpose, there has been no further effort to take an advantage from the recent progress in the plasma field. Here, we developed a nonthermal atmospheric plasma jet system as an alternative tool for treatment of surfaces. The low-temperature plasma is a nonequilibrium system that has been widely used in biomedical area. Unlike conventional glow discharge systems, the plasma jet system successfully cleans and introduces hydrophilicity on the grid surface in the ambient environment without a vacuum. Therefore, we anticipate that the plasma jet system will have numerous benefits, such as convenience and versatility, as well as having potential applications in surface modification for both negative-stain and cryo-EM grid treatment.
History
DepositionFeb 16, 2022-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateApr 20, 2022-
Current statusApr 20, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26216.png

Downloads & links

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Map

FileDownload / File: emd_26216.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0275 Å
Density
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-2.7729049 - 4.9834204
Average (Standard dev.)0.007037926 (±0.15166478)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 263.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : The ternary complex of two subunits of MMOH_alpha, MMOH_beta, and...

EntireName: The ternary complex of two subunits of MMOH_alpha, MMOH_beta, and MMOH_gamma
Components
  • Complex: The ternary complex of two subunits of MMOH_alpha, MMOH_beta, and MMOH_gamma

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Supramolecule #1: The ternary complex of two subunits of MMOH_alpha, MMOH_beta, and...

SupramoleculeName: The ternary complex of two subunits of MMOH_alpha, MMOH_beta, and MMOH_gamma
type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Methylococcus capsulatus str. Texas = ATCC 19069 (bacteria)
Molecular weightTheoretical: 215 KDa

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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

BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 362000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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