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- EMDB-10716: head domain of Tsr1-FPZ pre-40S particle: structural class 1 (H1) -

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Basic information

Entry
Database: EMDB / ID: EMD-10716
Titlehead domain of Tsr1-FPZ pre-40S particle: structural class 1 (H1)
Map dataH1-Tsr1FPZ: head of yeast Tsr1-FPZ pre-40S particle -structural class 1 focused classification (with signal subtraction) on the head, structural class 1
Sample
  • Complex: early cytoplasmic yeast pre-40S particle (purified using Tsr1 as bait)
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.84 Å
AuthorsShayan R / Plassart L / Plisson-Chastang C
Funding support France, 1 items
OrganizationGrant numberCountry
French National Research AgencyANR 16-CE11-0029 France
CitationJournal: Molecules / Year: 2020
Title: Good Vibrations: Structural Remodeling of Maturing Yeast Pre-40S Ribosomal Particles Followed by Cryo-Electron Microscopy.
Authors: Ramtin Shayan / Dana Rinaldi / Natacha Larburu / Laura Plassart / Stéphanie Balor / David Bouyssié / Simon Lebaron / Julien Marcoux / Pierre-Emmanuel Gleizes / Célia Plisson-Chastang /
Abstract: Assembly of eukaryotic ribosomal subunits is a very complex and sequential process that starts in the nucleolus and finishes in the cytoplasm with the formation of functional ribosomes. Over the past ...Assembly of eukaryotic ribosomal subunits is a very complex and sequential process that starts in the nucleolus and finishes in the cytoplasm with the formation of functional ribosomes. Over the past few years, characterization of the many molecular events underlying eukaryotic ribosome biogenesis has been drastically improved by the "resolution revolution" of cryo-electron microscopy (cryo-EM). However, if very early maturation events have been well characterized for both yeast ribosomal subunits, little is known regarding the final maturation steps occurring to the small (40S) ribosomal subunit. To try to bridge this gap, we have used proteomics together with cryo-EM and single particle analysis to characterize yeast pre-40S particles containing the ribosome biogenesis factor Tsr1. Our analyses lead us to refine the timing of the early pre-40S particle maturation steps. Furthermore, we suggest that after an early and structurally stable stage, the beak and platform domains of pre-40S particles enter a "vibrating" or "wriggling" stage, that might be involved in the final maturation of 18S rRNA as well as the fitting of late ribosomal proteins into their mature position.
History
DepositionFeb 28, 2020-
Header (metadata) releaseMar 18, 2020-
Map releaseMar 18, 2020-
UpdateMar 18, 2020-
Current statusMar 18, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10716.png

Downloads & links

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Map

FileDownload / File: emd_10716.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationH1-Tsr1FPZ: head of yeast Tsr1-FPZ pre-40S particle -structural class 1 focused classification (with signal subtraction) on the head, structural class 1
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 384.12 Å		1.07 Å/pix.
x 360 pix.
= 384.12 Å		1.07 Å/pix.
x 360 pix.
= 384.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.15440899 - 0.48276907
Average (Standard dev.)0.0014577705 (±0.012415009)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 384.12003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0671.0671.067
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z384.120384.120384.120
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.1540.4830.001

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Supplemental data

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Half map: yeast Tsr1-FPZ pre-40S particle H1 - focused classification...

Fileemd_10716_half_map_1.map
Annotationyeast Tsr1-FPZ pre-40S particle H1 - focused classification on the head, structural class 1 unfiltered half-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: yeast Tsr1-FPZ pre-40S particle H1 - focused classification...

Fileemd_10716_half_map_2.map
Annotationyeast Tsr1-FPZ pre-40S particle H1 - focused classification on the head, structural class 1 unfiltered 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 : early cytoplasmic yeast pre-40S particle (purified using Tsr1 as bait)

EntireName: early cytoplasmic yeast pre-40S particle (purified using Tsr1 as bait)
Components
  • Complex: early cytoplasmic yeast pre-40S particle (purified using Tsr1 as bait)

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Supramolecule #1: early cytoplasmic yeast pre-40S particle (purified using Tsr1 as bait)

SupramoleculeName: early cytoplasmic yeast pre-40S particle (purified using Tsr1 as bait)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#34
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 1.8 MDa

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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: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 292 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 29.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4v88

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 27227
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6fai

RefinementProtocol: OTHER

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