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- EMDB-16350: Enp1TAP_B, multibody refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-16350
TitleEnp1TAP_B, multibody refinement
Map dataEnp1TAP_B, multibody refinement
Sample
  • Complex: Enp1-TAP associated immature ribosomal particles from S. cerevisiae
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsMilkereit P / Poell G
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 960 Germany
CitationJournal: PLoS One / Year: 2023
Title: Impact of the yeast S0/uS2-cluster ribosomal protein rpS21/eS21 on rRNA folding and the architecture of small ribosomal subunit precursors.
Authors: Gisela Pöll / Joachim Griesenbeck / Herbert Tschochner / Philipp Milkereit /
Abstract: RpS0/uS2, rpS2/uS5, and rpS21/eS21 form a cluster of ribosomal proteins (S0-cluster) at the head-body junction near the central pseudoknot of eukaryotic small ribosomal subunits (SSU). Previous work ...RpS0/uS2, rpS2/uS5, and rpS21/eS21 form a cluster of ribosomal proteins (S0-cluster) at the head-body junction near the central pseudoknot of eukaryotic small ribosomal subunits (SSU). Previous work in yeast indicated that S0-cluster assembly is required for the stabilisation and maturation of SSU precursors at specific post-nucleolar stages. Here, we analysed the role of S0-cluster formation for rRNA folding. Structures of SSU precursors isolated from yeast S0-cluster expression mutants or control strains were analysed by cryogenic electron microscopy. The obtained resolution was sufficient to detect individual 2'-O-methyl RNA modifications using an unbiased scoring approach. The data show how S0-cluster formation enables the initial recruitment of the pre-rRNA processing factor Nob1 in yeast. Furthermore, they reveal hierarchical effects on the pre-rRNA folding pathway, including the final maturation of the central pseudoknot. Based on these structural insights we discuss how formation of the S0-cluster determines at this early cytoplasmic assembly checkpoint if SSU precursors further mature or are degraded.
History
DepositionDec 15, 2022-
Header (metadata) releaseDec 28, 2022-
Map releaseDec 28, 2022-
UpdateApr 12, 2023-
Current statusApr 12, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16350.png

Downloads & links

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Map

FileDownload / File: emd_16350.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEnp1TAP_B, multibody refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 400 pix.
= 387.2 Å		0.97 Å/pix.
x 400 pix.
= 387.2 Å		0.97 Å/pix.
x 400 pix.
= 387.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.968 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.005803086 - 0.035609238
Average (Standard dev.)0.0002894859 (±0.0014875261)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 387.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Enp1-TAP associated immature ribosomal particles from S. cerevisiae

EntireName: Enp1-TAP associated immature ribosomal particles from S. cerevisiae
Components
  • Complex: Enp1-TAP associated immature ribosomal particles from S. cerevisiae

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Supramolecule #1: Enp1-TAP associated immature ribosomal particles from S. cerevisiae

SupramoleculeName: Enp1-TAP associated immature ribosomal particles from S. cerevisiae
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#31
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288C-derivative laboratory strain

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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: 8
Component:
ConcentrationName
200.0 mMpotassium chloride
5.0 mMmagnesium acetate
20.0 mMTris pH8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 8575 / Average exposure time: 4.4 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 24592
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationSoftware - Name: RELION (ver. 4.0)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT

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