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- EMDB-40090: Unsupervised detection of proteasome in Rattus neuron -

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Basic information

Entry
Database: EMDB / ID: EMD-40090
TitleUnsupervised detection of proteasome in Rattus neuron
Map data
Sample
  • Complex: Proteasome
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 29.0 Å
AuthorsZeng X
Funding support United States, 8 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM134020 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103712 United States
National Science Foundation (NSF, United States)DBI-1949629 United States
National Science Foundation (NSF, United States)IIS-2007595 United States
National Science Foundation (NSF, United States)IIS-2211597 United States
National Science Foundation (NSF, United States)MCB-2205148 United States
The Mark Foundation19-044-ASP United States
David and Lucile Packard Foundation2019-69645 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: High-throughput cryo-ET structural pattern mining by unsupervised deep iterative subtomogram clustering.
Authors: Xiangrui Zeng / Anson Kahng / Liang Xue / Julia Mahamid / Yi-Wei Chang / Min Xu /
Abstract: Cryoelectron tomography directly visualizes heterogeneous macromolecular structures in their native and complex cellular environments. However, existing computer-assisted structure sorting approaches ...Cryoelectron tomography directly visualizes heterogeneous macromolecular structures in their native and complex cellular environments. However, existing computer-assisted structure sorting approaches are low throughput or inherently limited due to their dependency on available templates and manual labels. Here, we introduce a high-throughput template-and-label-free deep learning approach, Deep Iterative Subtomogram Clustering Approach (DISCA), that automatically detects subsets of homogeneous structures by learning and modeling 3D structural features and their distributions. Evaluation on five experimental cryo-ET datasets shows that an unsupervised deep learning based method can detect diverse structures with a wide range of molecular sizes. This unsupervised detection paves the way for systematic unbiased recognition of macromolecular complexes in situ.
History
DepositionMar 15, 2023-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateApr 19, 2023-
Current statusApr 19, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40090.png

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Map

FileDownload / File: emd_40090.map.gz / Format: CCP4 / Size: 85.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 13.68 Å
Density
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-1.712893 - 1.7336581
Average (Standard dev.)-0.013411207 (±0.20980456)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions282828
Spacing282828
CellA=B=C: 383.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_40090_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_40090_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 : Proteasome

EntireName: Proteasome
Components
  • Complex: Proteasome

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Supramolecule #1: Proteasome

SupramoleculeName: Proteasome / type: complex / ID: 1 / Chimera: Yes / Parent: 0
Source (natural)Organism: Rattus norvegicus (Norway 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-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 5.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 7 / Number images used: 38292
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 29.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.1) / Number subtomograms used: 1176

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