[English] 日本語
Yorodumi
- EMDB-10715: Yeast Tsr1-FPZ pre-40S particle - consensus structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10715
TitleYeast Tsr1-FPZ pre-40S particle - consensus structure
Map data
Sampleearly cytoplasmic yeast pre-40S particle (purified using Tsr1 as bait)
Function / homology
Function and homology information


positive regulation of RNA import into nucleus / EGO complex / ATP export / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U3 snoRNA binding / poly(A)+ mRNA export from nucleus / rRNA export from nucleus / preribosome, small subunit precursor / 90S preribosome ...positive regulation of RNA import into nucleus / EGO complex / ATP export / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U3 snoRNA binding / poly(A)+ mRNA export from nucleus / rRNA export from nucleus / preribosome, small subunit precursor / 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / snoRNA binding / rRNA methylation / 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) / ribosomal small subunit export from nucleus / ribonucleoprotein complex binding / maturation of SSU-rRNA / regulation of translational fidelity / response to osmotic stress / small-subunit processome / late endosome membrane / ribosomal small subunit biogenesis / proteasome assembly / positive regulation of translational fidelity / maintenance of translational fidelity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / rRNA processing / cytoplasmic stress granule / cytoplasmic translation / ribosome biogenesis / cellular response to oxidative stress / cytosolic small ribosomal subunit / unfolded protein binding / small ribosomal subunit / ribosome / rRNA binding / structural constituent of ribosome / non-specific serine/threonine protein kinase / translation / GTPase activity / protein kinase activity / mRNA binding / GTP binding / nucleolus / protein serine/threonine kinase activity / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Ribosomal protein S13-like, H2TH / Nucleic acid-binding, OB-fold / Ribosome biogenesis protein BMS1/TSR1, C-terminal / Low temperature viability protein Ltv1 / Bystin / S15/NS1, RNA-binding / Protein kinase-like domain superfamily / Zinc-binding ribosomal protein / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S12/S23 ...Ribosomal protein S13-like, H2TH / Nucleic acid-binding, OB-fold / Ribosome biogenesis protein BMS1/TSR1, C-terminal / Low temperature viability protein Ltv1 / Bystin / S15/NS1, RNA-binding / Protein kinase-like domain superfamily / Zinc-binding ribosomal protein / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S12/S23 / Ribosomal protein L23/L15e core domain superfamily / AARP2CN / Ribosomal protein S5, N-terminal / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S30 / KOW / RIO2 kinase winged helix domain, N-terminal / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S21e / Ribosomal protein S11 / Ribosomal protein S24e / Ribosomal protein S19/S15 / RNA-binding S4 domain / Ribosomal protein S25 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S5, C-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein L2, domain 2 / Ribosomal protein S4, conserved site / Winged helix-like DNA-binding domain superfamily / Ribosomal protein S2, eukaryotic / Ribosomal protein S15P / Ribosomal protein S19, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S8e/ribosomal biogenesis NSA2 / 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 S4/S9 / Ribosomal protein S19 conserved site / Ribosomal S24e conserved site / Ribosomal protein S17e, 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 S19e, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S13 / Ribosomal protein S2 / Ribosomal protein S10 / Ribosomal protein S19e domain superfamily / Ribosomal protein S17e-like superfamily / K Homology domain, type 1 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S4e, central domain superfamily / Winged helix DNA-binding 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 / Krr1, KH1 domain / Ribosomal protein S4, KOW domain / Ribosomal protein S14/S29 / Ribosomal protein S3Ae / Ribosomal protein S8 superfamily / Ribosomal protein S28e / Ribosomal protein S17e / Ribosomal protein S9 / Ribosomal protein S12e
40S ribosomal protein S0-A / 40S ribosomal protein S1-A / Protein LTV1 / 40S ribosomal protein S27-A / Essential nuclear protein 1 / 40S ribosomal protein S20 / Serine/threonine-protein kinase RIO2 / 40S ribosomal protein S29-A / 40S ribosomal protein S12 / 40S ribosomal protein S15 ...40S ribosomal protein S0-A / 40S ribosomal protein S1-A / Protein LTV1 / 40S ribosomal protein S27-A / Essential nuclear protein 1 / 40S ribosomal protein S20 / Serine/threonine-protein kinase RIO2 / 40S ribosomal protein S29-A / 40S ribosomal protein S12 / 40S ribosomal protein S15 / Ribosome biogenesis protein TSR1 / 40S ribosomal protein S25-A / 40S ribosomal protein S28-A / 40S ribosomal protein S5 / 40S ribosomal protein S7-A / 40S ribosomal protein S24-A / 40S ribosomal protein S2 / 40S ribosomal protein S22-A / 40S ribosomal protein S9-A / 40S ribosomal protein S17-A / 40S ribosomal protein S13 / 40S ribosomal protein S14-A / 40S ribosomal protein S19-A / 40S ribosomal protein S21-A / 40S ribosomal protein S23-A / 40S ribosomal protein S18-A / 40S ribosomal protein S30-A / 40S ribosomal protein S4-A / 40S ribosomal protein S6-A / 40S ribosomal protein S8-A / 40S ribosomal protein S11-A / 40S ribosomal protein S16-A / Pre-rRNA-processing protein PNO1
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.095
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.095
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_10715.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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
Contour LevelBy AUTHOR: 0.095 / Movie #1: 0.095
Minimum - Maximum-0.1967352 - 0.7277422
Average (Standard dev.)0.003251952 (±0.019508608)
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-0.1970.7280.003

-
Supplemental data

-
Half map: Yeast Tsr1-FPZ (wild type) pre-40S particle. Consensus cryo-EM...

Fileemd_10715_half_map_1.map
AnnotationYeast Tsr1-FPZ (wild type) pre-40S particle. Consensus cryo-EM map : unfiltered half-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: Yeast Tsr1-FPZ (wild type) pre-40S particle. Consensus cryo-EM...

Fileemd_10715_half_map_2.map
AnnotationYeast Tsr1-FPZ (wild type) pre-40S particle. Consensus cryo-EM map : unfiltered half-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

-
Entire early cytoplasmic yeast pre-40S particle (purified using Tsr1 as bait)

EntireName: early cytoplasmic yeast pre-40S particle (purified using Tsr1 as bait)
Number of components: 1

-
Component #1: protein, early cytoplasmic yeast pre-40S particle (purified using...

ProteinName: early cytoplasmic yeast pre-40S particle (purified using Tsr1 as bait)
Recombinant expression: No
MassTheoretical: 1.8 MDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 292 K / Humidity: 95 %

-
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: 29.4 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 74769
3D reconstructionAlgorithm: EXACT BACK PROJECTION / Software: RELION / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Input PDB model: 6FAI

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more