[English] 日本語
Yorodumi
- EMDB-6105: Cryo-EM Structure of the 80S-RAC complex from yeast -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6105
TitleCryo-EM Structure of the 80S-RAC complex from yeast
Map dataReconstruction of yeast 80S-RAC complex (Non-rotated state with higher RAC occupancy from Dataset RAC5, RAC9, RAC10)
Sample
  • Sample: Ribosome-associated complex (RAC) interacting with Saccharomyces cerevisiae 80S ribosome
  • Complex: Saccharomyces cerevisiae 80S ribosome
  • Protein or peptide: Ribosome-associated complex
Keywordsribosome-associated complex / co-translational chaperone / cryo-em / translation regulation / Zuotin / SSZ
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsZhang YX / Ma CY / Yuan Y / Zhu J / Li NN / Chen C / Wu S / Yu L / Lei JL / Gao N
CitationJournal: Nat Struct Mol Biol / Year: 2014
Title: Structural basis for interaction of a cotranslational chaperone with the eukaryotic ribosome.
Authors: Yixiao Zhang / Chengying Ma / Yi Yuan / Jing Zhu / Ningning Li / Chu Chen / Shan Wu / Li Yu / Jianlin Lei / Ning Gao /
Abstract: Cotranslational chaperones, ubiquitous in all living organisms, protect nascent polypeptides from aggregation and facilitate their de novo folding. Importantly, emerging data have also suggested that ...Cotranslational chaperones, ubiquitous in all living organisms, protect nascent polypeptides from aggregation and facilitate their de novo folding. Importantly, emerging data have also suggested that ribosome-associated cotranslational chaperones have active regulatory roles in modulating protein translation. By characterizing the structure of a type of eukaryotic cotranslational chaperone, the ribosome-associated complex (RAC) from Saccharomyces cerevisiae, we show that RAC cross-links two ribosomal subunits, through a single long α-helix, to limit the predominant intersubunit rotation required for peptide elongation. We further demonstrate that any changes in the continuity, length or rigidity of this middle α-helix impair RAC function in vivo. Our results suggest a new mechanism in which RAC directly regulates protein translation by mechanically coupling cotranslational folding with the peptide-elongation cycle, and they lay the foundation for further exploration of regulatory roles of RAC in translation control.
History
DepositionSep 28, 2014-
Header (metadata) releaseOct 22, 2014-
Map releaseOct 22, 2014-
UpdateFeb 24, 2016-
Current statusFeb 24, 2016Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0045
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_6105.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of yeast 80S-RAC complex (Non-rotated state with higher RAC occupancy from Dataset RAC5, RAC9, RAC10)
Voxel sizeX=Y=Z: 1.16 Å
Density
Contour LevelBy AUTHOR: 0.0045 / Movie #1: 0.0045
Minimum - Maximum-0.02530606 - 0.06713509
Average (Standard dev.)0.00007339 (±0.0088381)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 417.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z417.600417.600417.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0250.0670.000

-
Supplemental data

-
Sample components

-
Entire : Ribosome-associated complex (RAC) interacting with Saccharomyces ...

EntireName: Ribosome-associated complex (RAC) interacting with Saccharomyces cerevisiae 80S ribosome
Components
  • Sample: Ribosome-associated complex (RAC) interacting with Saccharomyces cerevisiae 80S ribosome
  • Complex: Saccharomyces cerevisiae 80S ribosome
  • Protein or peptide: Ribosome-associated complex

-
Supramolecule #1000: Ribosome-associated complex (RAC) interacting with Saccharomyces ...

SupramoleculeName: Ribosome-associated complex (RAC) interacting with Saccharomyces cerevisiae 80S ribosome
type: sample / ID: 1000 / Number unique components: 2

-
Supramolecule #1: Saccharomyces cerevisiae 80S ribosome

SupramoleculeName: Saccharomyces cerevisiae 80S ribosome / type: complex / ID: 1 / Recombinant expression: Yes / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Macromolecule #1: Ribosome-associated complex

MacromoleculeName: Ribosome-associated complex / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Details: 20mM Hepes-KOH, 120mM KOAc, 10mM Mg(OAc)2
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateJan 9, 2013
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Number real images: 8501 / Average electron dose: 20 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 24619
DetailsParticles selected by spider. Classification and Refinement with Relion.
FSC plot (resolution estimation)

+
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