[English] 日本語
Yorodumi
- EMDB-1811: Yeast 80S ribosome stalled by a stem-loop containing mRNA in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1811
TitleYeast 80S ribosome stalled by a stem-loop containing mRNA in complex with Dom34-Hbs1. The dataset is computationally sorted for presence of P-site tRNA and Dom34-Hbs1.
Map dataThis map represents a cryo-EM reconstruction of yeast 80S ribosome stalled by a stable stem-loop structure in complex with Dom34 and Hbs1. Additionally, it contains a P-site tRNA.
Sample
  • Sample: Stem-loop stalled yeast 80S ribosome in complex with Dom34-Hbs1 and P-site tRNA.
  • Complex: Saccharomyces cerevisiae 80S ribosome
  • Protein or peptide: Hbs1p
  • Protein or peptide: Dom34p
KeywordsRibosome / stalling / mRNA / P-site tRNA / no-go mRNA decay
Function / homology
Function and homology information


Eukaryotic Translation Elongation / RNA surveillance / Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / HSF1 activation / ribosome disassembly / Protein methylation / nonfunctional rRNA decay / positive regulation of translational initiation ...Eukaryotic Translation Elongation / RNA surveillance / Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / HSF1 activation / ribosome disassembly / Protein methylation / nonfunctional rRNA decay / positive regulation of translational initiation / translation elongation factor activity / Neutrophil degranulation / RNA endonuclease activity / rescue of stalled ribosome / positive regulation of translation / meiotic cell cycle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / translation / cell division / GTPase activity / GTP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Translation release factor pelota / HBS1-like protein, N-terminal / Pelota/DOM34, N-terminal domain / HBS1 N-terminus / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 ...Translation release factor pelota / HBS1-like protein, N-terminal / Pelota/DOM34, N-terminal domain / HBS1 N-terminus / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 / eRF1 domain 3 / eRF1_1 / GTP-eEF1A C-terminal domain-like / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / 50S ribosomal protein L30e-like / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Elongation factor 1 alpha-like protein / Protein DOM34
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsBecker T / Armache JP / Anger AM / Jarasch A / Villa E / Sieber H / AbdelMotaal B / Berninghausen O / Mielke T / Beckmann R
CitationJournal: Nat Struct Mol Biol / Year: 2011
Title: Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome.
Authors: Thomas Becker / Jean-Paul Armache / Alexander Jarasch / Andreas M Anger / Elizabeth Villa / Heidemarie Sieber / Basma Abdel Motaal / Thorsten Mielke / Otto Berninghausen / Roland Beckmann /
Abstract: No-go decay (NGD) is a mRNA quality-control mechanism in eukaryotic cells that leads to degradation of mRNAs stalled during translational elongation. The key factors triggering NGD are Dom34 and Hbs1. ...No-go decay (NGD) is a mRNA quality-control mechanism in eukaryotic cells that leads to degradation of mRNAs stalled during translational elongation. The key factors triggering NGD are Dom34 and Hbs1. We used cryo-EM to visualize NGD intermediates resulting from binding of the Dom34-Hbs1 complex to stalled ribosomes. At subnanometer resolution, all domains of Dom34 and Hbs1 were identified, allowing the docking of crystal structures and homology models. Moreover, the close structural similarity of Dom34 and Hbs1 to eukaryotic release factors (eRFs) enabled us to propose a model for the ribosome-bound eRF1-eRF3 complex. Collectively, our data provide structural insights into how stalled mRNA is recognized on the ribosome and how the eRF complex can simultaneously recognize stop codons and catalyze peptide release.
History
DepositionOct 25, 2010-
Header (metadata) releaseMay 27, 2011-
Map releaseMay 27, 2011-
UpdateSep 10, 2014-
Current statusSep 10, 2014Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3izq
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3izq
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3izq
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1811.gif

Downloads & links

-
Map

FileDownload / File: emd_1811.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis map represents a cryo-EM reconstruction of yeast 80S ribosome stalled by a stable stem-loop structure in complex with Dom34 and Hbs1. Additionally, it contains a P-site tRNA.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.24 Å/pix.
x 368 pix.
= 455.4 Å		1.24 Å/pix.
x 368 pix.
= 455.4 Å		1.24 Å/pix.
x 368 pix.
= 455.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-1.61734 - 2.59104
Average (Standard dev.)0.0163218 (±0.174673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-184-184-183
Dimensions368368368
Spacing368368368
CellA=B=C: 455.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.23751.23751.2375
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z455.400455.400455.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S213
start NC/NR/NS-184-184-183
NC/NR/NS368368368
D min/max/mean-1.6172.5910.016

-
Supplemental data

-
Sample components

-
Entire : Stem-loop stalled yeast 80S ribosome in complex with Dom34-Hbs1 a...

EntireName: Stem-loop stalled yeast 80S ribosome in complex with Dom34-Hbs1 and P-site tRNA.
Components
  • Sample: Stem-loop stalled yeast 80S ribosome in complex with Dom34-Hbs1 and P-site tRNA.
  • Complex: Saccharomyces cerevisiae 80S ribosome
  • Protein or peptide: Hbs1p
  • Protein or peptide: Dom34p

-
Supramolecule #1000: Stem-loop stalled yeast 80S ribosome in complex with Dom34-Hbs1 a...

SupramoleculeName: Stem-loop stalled yeast 80S ribosome in complex with Dom34-Hbs1 and P-site tRNA.
type: sample / ID: 1000
Details: Mammalian Sec61 was added to saturate the hydrophobic signal sequence present in the nascent polypeptide chain.
Oligomeric state: One ribosome / Number unique components: 3
Molecular weightTheoretical: 3.3 MDa

-
Supramolecule #1: Saccharomyces cerevisiae 80S ribosome

SupramoleculeName: Saccharomyces cerevisiae 80S ribosome / type: complex / ID: 1 / Name.synonym: yeast 80S ribosome
Details: The mRNA stem-loop structure is not visible in the Cryo-EM reconstruction indicating its flexibility
Ribosome-details: ribosome-eukaryote: ALL
Molecular weightExperimental: 3.2 MDa / Theoretical: 3.2 MDa

-
Macromolecule #1: Hbs1p

MacromoleculeName: Hbs1p / type: protein_or_peptide / ID: 1 / Name.synonym: Hbs1p / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Bakers's yeast / Location in cell: cytosol
Molecular weightExperimental: 68 KDa / Theoretical: 68 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET28b

-
Macromolecule #2: Dom34p

MacromoleculeName: Dom34p / type: protein_or_peptide / ID: 2 / Name.synonym: Dom34p / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Bakers's yeast / Location in cell: cytosol
Molecular weightExperimental: 44 KDa / Theoretical: 44 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET21a

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.02 mg/mL
BufferpH: 7
Details: 20 mM Tris/HCl, pH 7.0, 80 mM NaCl, 97 mM KOAc, 10 mM Mg(OAc)2, 1.5 mM DTT, 0.02 % Nikkol, 1.8 % Glycerol, 0.01 mg/ml Cycloheximide, 500 0.5 mM GDPNP, 0.3 % Digitonin
GridDetails: Quantifoil Grid with 2 nm carbon on top
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot
Method: Blotted for 10 seconds before plunging, used 2 layer of filter paper

-
Electron microscopy

MicroscopeFEI POLARA 300
TemperatureAverage: 84 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100000 times magnification
Image recordingCategory: CCD / Film or detector model: KODAK SO-163 FILM / Digitization - Sampling interval: 4.76 µm / Number real images: 78 / Average electron dose: 25 e/Å2
Details: Scanned with a Heidelberg PrimeScan drum scanner at 5334 dpi
Od range: 1.2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.78 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 39000
Sample stageSpecimen holder: FEI Polara Cartridge System / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

DetailsMammalian Sec61 complex was added to the sample to saturate the hydrophobic nascent chain
CTF correctionDetails: CTF correction on the level of 3D volumes (SPIDER TF CTS command)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER
Details: The dataset was sorted according to presence of Dom34-Hbs1 complex and P-site tRNA.
Number images used: 38400

-
Atomic model buiding 1

Initial modelPDB ID:

2vgm

SoftwareName: Molecular Dynamics based flexible fitting MDFF
DetailsRigid body fitting of individual domains using Coot followed by MDFF
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-3izq:
Structure of the Dom34-Hbs1-GDPNP complex bound to a translating ribosome

-
Atomic model buiding 2

Initial modelPDB ID:

2qi2

SoftwareName: Molecular Dynamics based flexible fitting MDFF
DetailsRigid body fitting of individual domains using Coot followed by MDFF
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-3izq:
Structure of the Dom34-Hbs1-GDPNP complex bound to a translating ribosome

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

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. 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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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