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- EMDB-33074: neighboring ribosomes cluster1 -

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Basic information

Entry
Database: EMDB / ID: EMD-33074
Titleneighboring ribosomes cluster1
Map data
Sample
  • Complex: neighboring ribosomes cluter1
Biological speciesRattus (rat)
Methodsubtomogram averaging / cryo EM / Resolution: 27.36 Å
AuthorsJiang W / Guo Q
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res / Year: 2022
Title: A transformation clustering algorithm and its application in polyribosomes structural profiling.
Authors: Wenhong Jiang / Jonathan Wagner / Wenjing Du / Juergen Plitzko / Wolfgang Baumeister / Florian Beck / Qiang Guo /
Abstract: Improvements in cryo-electron tomography sample preparation, electron-microscopy instrumentations, and image processing algorithms have advanced the structural analysis of macromolecules in situ. ...Improvements in cryo-electron tomography sample preparation, electron-microscopy instrumentations, and image processing algorithms have advanced the structural analysis of macromolecules in situ. Beyond such analyses of individual macromolecules, the study of their interactions with functionally related neighbors in crowded cellular habitats, i.e. 'molecular sociology', is of fundamental importance in biology. Here we present a NEighboring Molecule TOpology Clustering (NEMO-TOC) algorithm. We optimized this algorithm for the detection and profiling of polyribosomes, which play both constitutive and regulatory roles in gene expression. Our results suggest a model where polysomes are formed by connecting multiple nonstochastic blocks, in which translation is likely synchronized.
History
DepositionMar 16, 2022-
Header (metadata) releaseJun 29, 2022-
Map releaseJun 29, 2022-
UpdateSep 21, 2022-
Current statusSep 21, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33074.png

Downloads & links

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Map

FileDownload / File: emd_33074.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 6.84 Å
Density
Contour LevelBy AUTHOR: 0.583
Minimum - Maximum-0.81401014 - 2.2717671
Average (Standard dev.)0.0153898345 (±0.13558511)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 1231.2001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33074_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

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Half map: #1

Fileemd_33074_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_33074_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : neighboring ribosomes cluter1

EntireName: neighboring ribosomes cluter1
Components
  • Complex: neighboring ribosomes cluter1

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Supramolecule #1: neighboring ribosomes cluter1

SupramoleculeName: neighboring ribosomes cluter1 / type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Rattus (rat)

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 27.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 3124
ExtractionNumber tomograms: 18 / Number images used: 11547
Final angle assignmentType: MAXIMUM LIKELIHOOD

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