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- EMDB-15311: Dedicated chaperone at the ribosome safeguards the proteostasis n... -

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Basic information

Entry
Database: EMDB / ID: EMD-15311
TitleDedicated chaperone at the ribosome safeguards the proteostasis network during eEF1A biogenesis
Map dataoverall map, unsharpened
Sample
  • Complex: Chp1-80S ribosomal complexes
KeywordsCHP1 / Ribosome / Complex
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMinoia M / Quintana-Cordero J / Katharina J / Kotan I / Turnbull KJ / Masser AE / Merker D / Gouarin E / Ehrenbolger K / Barandun J ...Minoia M / Quintana-Cordero J / Katharina J / Kotan I / Turnbull KJ / Masser AE / Merker D / Gouarin E / Ehrenbolger K / Barandun J / Hauryliuk V / Bukau B / Kramer G / Andreasson C
Funding support Sweden, European Union, Estonia, 4 items
OrganizationGrant numberCountry
Swedish Research Council2019-02011 / 2017-03783 / 2021-01146 Sweden
European Research Council (ERC)ERC Starting Grant PolTube 948655European Union
European Regional Development FundEuropean Union
Estonian Research CouncilPRG335 Estonia
CitationJournal: To Be Published
Title: Dedicated chaperone at the ribosome safeguards the proteostasis network during eEF1A biogenesis
Authors: Minoia M / Quintana-Cordero J / Katharina J / Kotan I / Turnbull KJ / Masser AE / Merker D / Gouarin E / Ehrenbolger K / Barandun J / Hauryliuk V / Bukau B / Kramer G / Andreasson C
History
DepositionJul 4, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJul 12, 2023-
Current statusJul 12, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15311.png

Downloads & links

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Map

FileDownload / File: emd_15311.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationoverall map, unsharpened
Voxel sizeX=Y=Z: 1.64 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.040800534 - 0.118021086
Average (Standard dev.)0.00056070497 (±0.0059150616)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 459.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: focused map

Fileemd_15311_additional_1.map
Annotationfocused map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: focused half map 1

Fileemd_15311_additional_2.map
Annotationfocused half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused half map 2

Fileemd_15311_additional_3.map
Annotationfocused half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: overall half map 1

Fileemd_15311_half_map_1.map
Annotationoverall half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: overall half map 2

Fileemd_15311_half_map_2.map
Annotationoverall half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chp1-80S ribosomal complexes

EntireName: Chp1-80S ribosomal complexes
Components
  • Complex: Chp1-80S ribosomal complexes

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Supramolecule #1: Chp1-80S ribosomal complexes

SupramoleculeName: Chp1-80S ribosomal complexes / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BY4741

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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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: 1.7 µm / Nominal defocus min: 0.5 µm
DetailsData was collected at a pixel size of 0.82
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average exposure time: 3.0 sec. / Average electron dose: 33.7 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 240043
Startup modelType of model: OTHER
Details: RELION-3.1 Stochastic Gradient Descent (SGD) algorithm
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 86197

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