EMDB-4218: Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit, ...

Basic information

• Entry: Database: EMDB / ID: EMD-4218
• Title: Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit, classified for Dim1

Sample

• Complex: Cytoplasmic pre-40S ribosomal subunit, classified for Dim1

Function / homology

Function:

positive regulation of RNA import into nucleus / Ragulator complex / ATP export / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / endocytic recycling / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / mTORC1-mediated signalling / ribosome-associated ubiquitin-dependent protein catabolic process / Protein hydroxylation / GDP-dissociation inhibitor activity / : / U3 snoRNA binding / poly(A)+ mRNA export from nucleus / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / response to osmotic stress / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / snoRNA binding / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal small subunit export from nucleus / L13a-mediated translational silencing of Ceruloplasmin expression / translation regulator activity / G-protein alpha-subunit binding / proteasome assembly / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / ribonucleoprotein complex binding / rescue of stalled ribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) endonuclease activity / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytoplasmic stress granule / cytosolic small ribosomal subunit / unfolded protein binding / ribosome binding / protein transport / late endosome / ribosome biogenesis / late endosome membrane / cellular response to oxidative stress / cytoplasmic translation / small ribosomal subunit / negative regulation of translation / rRNA binding / non-specific serine/threonine protein kinase / ribosome / protein kinase activity / structural constituent of ribosome / positive regulation of protein phosphorylation / translation / G protein-coupled receptor signaling pathway / phosphorylation / negative regulation of gene expression / protein serine kinase activity / mRNA binding / GTPase activity / protein serine/threonine kinase activity / GTP binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm

Domain/homology:

Low temperature viability protein Ltv1 / Low temperature viability protein / Serine/threonine-protein kinase Rio2 / RIO2 kinase winged helix domain, N-terminal / Rio2, N-terminal / RIO kinase / RIO-like kinase / RIO1 family / Krr1, KH1 domain / Krr1 KH1 domain / Bystin / Bystin / Ribosome biogenesis protein BMS1/TSR1, C-terminal / AARP2CN / Bms1/Tsr1-type G domain / Ribosome biogenesis protein Bms1/Tsr1 / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / AARP2CN (NUC121) domain / Bms1-type guanine nucleotide-binding (G) domain profile. / AARP2CN (NUC121) domain / Protein of unknown function (DUF663) / K Homology domain, type 1 superfamily / : / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S17e, conserved site / : / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / Ribosomal protein S19A/S15e / Ribosomal protein S21e signature. / Ribosomal protein S30 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal_S17 N-terminal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein S7e / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / RS4NT (NUC023) domain / Ribosomal protein S27 / Ribosomal S3Ae family / Ribosomal protein S17e signature. / Ribosomal protein S28e / Ribosomal family S4e / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S7e signature. / Ribosomal protein S6e / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e signature. / Ribosomal protein S8e signature. / Ribosomal S24e conserved site

Component:

Small ribosomal subunit protein uS4A / Small ribosomal subunit protein eS17A / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein eS21A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Small ribosomal subunit protein uS17A / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS13A / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS7A / Small ribosomal subunit protein uS2A / Small ribosomal subunit protein eS1A / Protein LTV1 / Small ribosomal subunit protein eS27A / Small ribosomal subunit protein RACK1 / Essential nuclear protein 1 / Small ribosomal subunit protein uS10 / Serine/threonine-protein kinase RIO2 / Small ribosomal subunit protein uS14A / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS19 / Ribosome biogenesis protein TSR1 / Small ribosomal subunit protein eS25A / Small ribosomal subunit protein eS28A / Pre-rRNA-processing protein PNO1

• Biological species: Saccharomyces cerevisiae (brewer's yeast)
• Method: single particle reconstruction / cryo EM / Resolution: 4.3 Å
• Authors: Scaiola A / Pena C / Weisser M / Boehringer D / Leibundgut M / Klingauf-Nerurkar P / Gerhardy S / Panse VG / Ban N
• Citation: Journal: 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 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.

History

Deposition	Dec 15, 2017	-
Header (metadata) release	Jan 17, 2018	-
Map release	Feb 28, 2018	-
Update	Apr 1, 2020	-
Current status	Apr 1, 2020	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_4218.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.39 Å

Density

Contour Level	By EMDB: 0.05 / Movie #1: 0.05
Minimum - Maximum	-0.09972754 - 0.28786635
Average (Standard dev.)	0.00090715743 (±0.010179055)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 320 320 320 Spacing 320 320 320
Cell	A=B=C: 444.8 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.39	1.39	1.39
M x/y/z	320	320	320
origin x/y/z	0.000	0.000	0.000
length x/y/z	444.800	444.800	444.800
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ	0	0	0
NX/NY/NZ	256	256	256
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	320	320	320
D min/max/mean	-0.100	0.288	0.001

Supplemental data

Half map: #1

• File: emd_4218_half_map_1.map

Half map: #2

• File: emd_4218_half_map_2.map

Sample components

Entire : Cytoplasmic pre-40S ribosomal subunit, classified for Dim1

• Entire: Name: Cytoplasmic pre-40S ribosomal subunit, classified for Dim1

Components

• Complex: Cytoplasmic pre-40S ribosomal subunit, classified for Dim1

Supramolecule #1: Cytoplasmic pre-40S ribosomal subunit, classified for Dim1

• Supramolecule: Name: Cytoplasmic pre-40S ribosomal subunit, classified for Dim1; type: complex / ID: 1 / Parent: 0
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.4
• Vitrification: Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
• Image recording: Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 40.0 e/Ų
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Initial angle assignment: Type: OTHER
• Final angle assignment: Type: OTHER
• Final reconstruction: Applied symmetry - Point group: C₁ (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 40044