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- EMDB-20211: Subunit joining exposes nascent pre-40S rRNA for processing and q... -

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Basic information

Entry
Database: EMDB / ID: EMD-20211
TitleSubunit joining exposes nascent pre-40S rRNA for processing and quality control
Map data60S subunit of 80S-like ribosome
Sample
  • Complex: 60S subunit of 80S-like ribosome
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsRai J / Parker MD / Ghalei H / Johnson MC / Karbstein K / Stroupe ME
Funding support United States, 3 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute55108536 United States
National Institutes of Health/National Institute of General Medical SciencesR01-GM117093 United States
National Institutes of Health/National Institute of General Medical SciencesR01-GM086451 United States
CitationJournal: RNA / Year: 2021
Title: An open interface in the pre-80S ribosome coordinated by ribosome assembly factors Tsr1 and Dim1 enables temporal regulation of Fap7.
Authors: Jay Rai / Melissa D Parker / Haina Huang / Stefan Choy / Homa Ghalei / Matthew C Johnson / Katrin Karbstein / M Elizabeth Stroupe /
Abstract: During their maturation, nascent 40S subunits enter a translation-like quality control cycle, where they are joined by mature 60S subunits to form 80S-like ribosomes. While these assembly ...During their maturation, nascent 40S subunits enter a translation-like quality control cycle, where they are joined by mature 60S subunits to form 80S-like ribosomes. While these assembly intermediates are essential for maturation and quality control, how they form, and how their structure promotes quality control, remains unknown. To address these questions, we determined the structure of an 80S-like ribosome assembly intermediate to an overall resolution of 3.4 Å. The structure, validated by biochemical data, resolves a large body of previously paradoxical data and illustrates how assembly and translation factors cooperate to promote the formation of an interface that lacks many mature subunit contacts but is stabilized by the universally conserved methyltransferase Dim1. We also show how Tsr1 enables this interface by blocking the canonical binding of eIF5B to 40S subunits, while maintaining its binding to 60S. The structure also shows how this interface leads to unfolding of the platform, which allows for temporal regulation of the ATPase Fap7, thus linking 40S maturation to quality control during ribosome assembly.
History
DepositionMay 7, 2019-
Header (metadata) releaseJun 19, 2019-
Map releaseNov 25, 2020-
UpdateJun 9, 2021-
Current statusJun 9, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0067
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0067
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20211.png

Downloads & links

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Map

FileDownload / File: emd_20211.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation60S subunit of 80S-like ribosome
Voxel sizeX=Y=Z: 1.24 Å
Density
Contour LevelBy AUTHOR: 0.0067 / Movie #1: 0.0067
Minimum - Maximum-0.014216832 - 0.047586642
Average (Standard dev.)0.00050149194 (±0.0029103516)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 476.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.241.241.24
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z476.160476.160476.160
α/β/γ90.00090.00090.000
start NX/NY/NZ727265
NX/NY/NZ157157169
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0140.0480.001

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Supplemental data

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Sample components

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Entire : 60S subunit of 80S-like ribosome

EntireName: 60S subunit of 80S-like ribosome
Components
  • Complex: 60S subunit of 80S-like ribosome

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Supramolecule #1: 60S subunit of 80S-like ribosome

SupramoleculeName: 60S subunit of 80S-like ribosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: 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: 6.8
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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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
Image recordingFilm or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Detector mode: COUNTING / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90692

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