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- EMDB-41221: Cryo-electron tomography reconstruction of M. pneumoniae 70S ribo... -

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Basic information

Entry
Database: EMDB / ID: EMD-41221
TitleCryo-electron tomography reconstruction of M. pneumoniae 70S ribosome in classical non-rotated state with L1 open, obtained from EMPIAR-10499 dataset by constrained classification
Map data
Sample
  • Complex: M. pneumoniae 70S ribosome in the non-rotated state with L1 open
Keywordsribosome / non-rotated / cryo-ET / 70S
Biological speciesMycoplasmoides pneumoniae 19294 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 9.3 Å
AuthorsZhou Y / Liu HF / Bartesaghi A
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM141223 United States
Chan Zuckerberg InitiativeVisual Proteomics Imaging United States
CitationJournal: Nat Methods / Year: 2023
Title: nextPYP: a comprehensive and scalable platform for characterizing protein variability in situ using single-particle cryo-electron tomography.
Authors: Hsuan-Fu Liu / Ye Zhou / Qinwen Huang / Jonathan Piland / Weisheng Jin / Justin Mandel / Xiaochen Du / Jeffrey Martin / Alberto Bartesaghi /
Abstract: Single-particle cryo-electron tomography is an emerging technique capable of determining the structure of proteins imaged within the native context of cells at molecular resolution. While high- ...Single-particle cryo-electron tomography is an emerging technique capable of determining the structure of proteins imaged within the native context of cells at molecular resolution. While high-throughput techniques for sample preparation and tilt-series acquisition are beginning to provide sufficient data to allow structural studies of proteins at physiological concentrations, the complex data analysis pipeline and the demanding storage and computational requirements pose major barriers for the development and broader adoption of this technology. Here, we present a scalable, end-to-end framework for single-particle cryo-electron tomography data analysis from on-the-fly pre-processing of tilt series to high-resolution refinement and classification, which allows efficient analysis and visualization of datasets with hundreds of tilt series and hundreds of thousands of particles. We validate our approach using in vitro and cellular datasets, demonstrating its effectiveness at achieving high-resolution and revealing conformational heterogeneity in situ. The framework is made available through an intuitive and easy-to-use computer application, nextPYP ( http://nextpyp.app ).
History
DepositionJul 7, 2023-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41221.png

Downloads & links

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Map

FileDownload / File: emd_41221.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 3.4 Å
Density
Contour LevelBy AUTHOR: 2.25
Minimum - Maximum-4.52246 - 8.585523
Average (Standard dev.)0.09660877 (±0.5930177)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41221_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41221_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : M. pneumoniae 70S ribosome in the non-rotated state with L1 open

EntireName: M. pneumoniae 70S ribosome in the non-rotated state with L1 open
Components
  • Complex: M. pneumoniae 70S ribosome in the non-rotated state with L1 open

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Supramolecule #1: M. pneumoniae 70S ribosome in the non-rotated state with L1 open

SupramoleculeName: M. pneumoniae 70S ribosome in the non-rotated state with L1 open
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mycoplasmoides pneumoniae 19294 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 3.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 65 / Number images used: 18165
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 5449
FSC plot (resolution estimation)

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