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- EMDB-41211: Cryo-electron tomography reconstruction of mammalian 80S ribosome... -

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Basic information

Entry
Database: EMDB / ID: EMD-41211
TitleCryo-electron tomography reconstruction of mammalian 80S ribosome in the non-rotated state with P, A/T-site tRNA from EMPIAR-10064 dataset by constrained classification.
Map data
Sample
  • Complex: Mammalian 80S ribosome in the non-rotated state with P-site tRNA
Keywordsribosome / classification / cryoET / non-rotated / P-site
Biological speciesOryctolagus cuniculus (rabbit)
Methodsubtomogram averaging / cryo EM / Resolution: 10.0 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_41211.png

Downloads & links

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Map

FileDownload / File: emd_41211.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
2.62 Å/pix.
x 256 pix.
= 670.72 Å		2.62 Å/pix.
x 256 pix.
= 670.72 Å		2.62 Å/pix.
x 256 pix.
= 670.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.62 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.94
Minimum - Maximum-4.44498 - 7.19024
Average (Standard dev.)0.0284341 (±0.35056326)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 670.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41211_half_map_1.map
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Half map: #2

Fileemd_41211_half_map_2.map
Projections & Slices
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Sample components

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Entire : Mammalian 80S ribosome in the non-rotated state with P-site tRNA

EntireName: Mammalian 80S ribosome in the non-rotated state with P-site tRNA
Components
  • Complex: Mammalian 80S ribosome in the non-rotated state with P-site tRNA

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Supramolecule #1: Mammalian 80S ribosome in the non-rotated state with P-site tRNA

SupramoleculeName: Mammalian 80S ribosome in the non-rotated state with P-site tRNA
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.7 µm / Nominal defocus min: 2.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 920
ExtractionNumber tomograms: 4 / Number images used: 4384
Final 3D classificationNumber classes: 5
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5lzs


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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