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- EMDB-45266: Structure of 70S ribosome from EMPIAR-10499 -

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Basic information

Entry
Database: EMDB / ID: EMD-45266
TitleStructure of 70S ribosome from EMPIAR-10499
Map data
Sample
  • Complex: 70S ribosome
Keywordsribosome / tomography / 70S
Biological speciesMycoplasmoides pneumoniae 19294 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 5.4 Å
AuthorsZhou Y / Huang QW / Bartesaghi A
Funding support United States, 1 items
OrganizationGrant numberCountry
Chan Zuckerberg InitiativeVisual Proteomics Imaging United States
CitationJournal: Nat Methods / Year: 2024
Title: MiLoPYP: self-supervised molecular pattern mining and particle localization in situ.
Authors: Qinwen Huang / Ye Zhou / Alberto Bartesaghi /
Abstract: Cryo-electron tomography allows the routine visualization of cellular landscapes in three dimensions at nanometer-range resolutions. When combined with single-particle tomography, it is possible to ...Cryo-electron tomography allows the routine visualization of cellular landscapes in three dimensions at nanometer-range resolutions. When combined with single-particle tomography, it is possible to obtain near-atomic resolution structures of frequently occurring macromolecules within their native environment. Two outstanding challenges associated with cryo-electron tomography/single-particle tomography are the automatic identification and localization of proteins, tasks that are hindered by the molecular crowding inside cells, imaging distortions characteristic of cryo-electron tomography tomograms and the sheer size of tomographic datasets. Current methods suffer from low accuracy, demand extensive and time-consuming manual labeling or are limited to the detection of specific types of proteins. Here, we present MiLoPYP, a two-step dataset-specific contrastive learning-based framework that enables fast molecular pattern mining followed by accurate protein localization. MiLoPYP's ability to effectively detect and localize a wide range of targets including globular and tubular complexes as well as large membrane proteins, will contribute to streamline and broaden the applicability of high-resolution workflows for in situ structure determination.
History
DepositionJun 8, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45266.png

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Map

FileDownload / File: emd_45266.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.7 Å/pix.
x 384 pix.
= 652.8 Å		1.7 Å/pix.
x 384 pix.
= 652.8 Å		1.7 Å/pix.
x 384 pix.
= 652.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.7 Å
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Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.4832704 - 1.983583
Average (Standard dev.)0.000009938075 (±0.08043478)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 652.80005 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45266_msk_1.map
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Half map: #1

Fileemd_45266_half_map_1.map
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Half map: #2

Fileemd_45266_half_map_2.map
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Sample components

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Entire : 70S ribosome

EntireName: 70S ribosome
Components
  • Complex: 70S ribosome

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Supramolecule #1: 70S ribosome

SupramoleculeName: 70S ribosome / 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 stateparticle

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Sample preparation

BufferpH: 7
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: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 17381
ExtractionNumber tomograms: 65 / Number images used: 23285
Final angle assignmentType: MAXIMUM LIKELIHOOD

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