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- EMDB-4217: Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit, ... -

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Entry
Database: EMDB / ID: 4217
TitleStructure of a eukaryotic cytoplasmic pre-40S ribosomal subunit, classified for Enp1
Map data
SampleCytoplasmic pre-40S ribosomal subunit, classified for Enp1:
Function / homologyRibosomal protein S7, conserved site / Ribosomal protein S3, C-terminal domain superfamily / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / Serine/threonine-protein kinase Rio2 / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal ...Ribosomal protein S7, conserved site / Ribosomal protein S3, C-terminal domain superfamily / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / Serine/threonine-protein kinase Rio2 / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8 superfamily / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Ribosomal protein S17e-like superfamily / K Homology domain, type 1 superfamily / Ribosomal protein S10 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S19e domain superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S21e superfamily / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosome biogenesis protein Bms1/Tsr1 / Pre-rRNA-processing protein PNO1-like / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal protein S3, C-terminal domain / Ribosomal protein S19 / Ribosomal protein S2, eukaryotic / 30s ribosomal protein S13, C-terminal / Ribosomal protein S15 / Ribosomal protein S21e, conserved site / WD40/YVTN repeat-like-containing domain superfamily / K homology domain-like, alpha/beta / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S7 domain / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S8e, conserved site / WD40 repeat, conserved site / Ribosomal protein S17, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / Ribosomal protein S15P / Ribosomal protein S19, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S14p/S29e / Ribosomal protein S2 / Ribosomal protein S13 family profile. / Ribosomal protein S6e signature. / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S11 signature. / Ribosomal protein S12 signature. / Ribosomal protein S17 signature. / Ribosomal protein S19 signature. / Ribosomal protein S9 signature. / Ribosomal protein S10 signature. / Ribosomal protein S15 signature. / Ribosomal protein S14 signature. / Ribosomal protein S4e signature. / Ribosomal protein S24e signature. / Ribosomal protein S3 signature. / Ribosomal protein S5 signature. / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19e signature. / Ribosomal protein S4 signature. / Ribosomal protein S13 signature. / Trp-Asp (WD) repeats signature. / Ribosomal protein S17e signature. / Ribosomal protein S7e signature. / Ribosomal protein S28e signature. / Ribosomal protein S2 signature 1. / Ribosomal protein S2 signature 2. / Ribosomal protein S21e signature. / Ribosomal protein S27e signature. / Ribosomal protein S12e signature. / Ribosomal protein S3Ae signature. / Ribosomal protein S8e signature. / Ribosomal_S17 N-terminal / Rio2, N-terminal
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 4 Å resolution
AuthorsScaiola A / Pena C / Weisser M / Boehringer D / Leibundgut M / Klingauf-Nerurkar P / Gerhardy S / Panse VG / Ban N
CitationJournal: EMBO J. / Year: 2018
Title: Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit.
Authors: Alain Scaiola / Cohue Peña / Melanie Weisser / Daniel Böhringer / Marc Leibundgut / Purnima Klingauf-Nerurkar / Stefan Gerhardy / Vikram Govind Panse / Nenad Ban
Abstract: Final maturation of eukaryotic ribosomes occurs in the cytoplasm and requires the sequential removal of associated assembly factors and processing of the immature 20S pre-RNA Using cryo-electron ...Final maturation of eukaryotic ribosomes occurs in the cytoplasm and requires the sequential removal of associated assembly factors and processing of the immature 20S pre-RNA Using cryo-electron microscopy (cryo-EM), we have determined the structure of a yeast cytoplasmic pre-40S particle in complex with Enp1, Ltv1, Rio2, Tsr1, and Pno1 assembly factors poised to initiate final maturation. The structure reveals that the pre-rRNA adopts a highly distorted conformation of its 3' major and 3' minor domains stabilized by the binding of the assembly factors. This observation is consistent with a mechanism that involves concerted release of the assembly factors orchestrated by the folding of the rRNA in the head of the pre-40S subunit during the final stages of maturation. Our results provide a structural framework for the coordination of the final maturation events that drive a pre-40S particle toward the mature form capable of engaging in translation.
DateDeposition: Dec 15, 2017 / Header (metadata) release: Jan 17, 2018 / Map release: Feb 28, 2018 / Last update: Apr 11, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4217.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.39 Å/pix.
= 444.8 Å
320 pix
1.39 Å/pix.
= 444.8 Å
320 pix
1.39 Å/pix.
= 444.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.1002325 - 0.29351974
Average (Standard dev.)0.00096798665 (0.011122892)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin0.00.00.0
Limit319.0319.0319.0
Spacing320320320
CellA=B=C: 444.8 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z444.800444.800444.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1000.2940.001

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Supplemental data

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Sample components

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Entire Cytoplasmic pre-40S ribosomal subunit, classified for Enp1

EntireName: Cytoplasmic pre-40S ribosomal subunit, classified for Enp1
Number of components: 1

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Component #1: protein, Cytoplasmic pre-40S ribosomal subunit, classified for Enp1

ProteinName: Cytoplasmic pre-40S ribosomal subunit, classified for Enp1
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: OTHER / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 39367
3D reconstructionSoftware: RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF
Details: This 3D class was resampled on the unclassified map so that the associated model fits in the density. The raw final reconstruction can be found as additional map in this entry.

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