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- EMDB-15228: RQT-bound 80S ribosome from S. cerevisiae (C1, raw consensus map) -

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Basic information

Entry
Database: EMDB / ID: EMD-15228
TitleRQT-bound 80S ribosome from S. cerevisiae (C1, raw consensus map)
Map datarefined map of the RQTc1 ribsome
Sample
  • Complex: ribosome with bound RQT components (Slh1, Cue3 and Rqt4)
    • Complex: RQT complex (Slh1, Cue3 and Rqt4)
    • Complex: ribosome
Keywordscollision / RNA binding / RQT / RQC / RIBOSOME
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsBest KM / Ikeuchi K / Kater L / Best DM / Musial J / Matsuo Y / Berninghausen O / Becker T / Inada T / Beckmann R
Funding supportEuropean Union, Germany, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)885711European Union
German Research Foundation (DFG)BE 1814/15-1 Germany
German Research Foundation (DFG)RTG1721 Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography.
Authors: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams /
Abstract: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.
History
DepositionJun 22, 2022-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateJun 21, 2023-
Current statusJun 21, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15228.png

Downloads & links

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Map

FileDownload / File: emd_15228.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrefined map of the RQTc1 ribsome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 560 pix.
= 585.2 Å		1.05 Å/pix.
x 560 pix.
= 585.2 Å		1.05 Å/pix.
x 560 pix.
= 585.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.653123 - 3.2884207
Average (Standard dev.)-0.0055903164 (±0.11298632)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 585.19995 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: halfmap 1

Fileemd_15228_half_map_1.map
Annotationhalfmap 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap 2

Fileemd_15228_half_map_2.map
Annotationhalfmap 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 : ribosome with bound RQT components (Slh1, Cue3 and Rqt4)

EntireName: ribosome with bound RQT components (Slh1, Cue3 and Rqt4)
Components
  • Complex: ribosome with bound RQT components (Slh1, Cue3 and Rqt4)
    • Complex: RQT complex (Slh1, Cue3 and Rqt4)
    • Complex: ribosome

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Supramolecule #1: ribosome with bound RQT components (Slh1, Cue3 and Rqt4)

SupramoleculeName: ribosome with bound RQT components (Slh1, Cue3 and Rqt4)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#82

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Supramolecule #2: RQT complex (Slh1, Cue3 and Rqt4)

SupramoleculeName: RQT complex (Slh1, Cue3 and Rqt4) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #80-#82
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: ribosome

SupramoleculeName: ribosome / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#79
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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 R3/3 / Material: COPPER / Support film - Material: CARBON
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 43.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 194186
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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