[English] 日本語
Yorodumi
- EMDB-2624: Recognition intermediate of Regulation of the mammalian elongatio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2624
TitleRecognition intermediate of Regulation of the mammalian elongation cycle by 40S subunit rolling: a eukaryotic-specific ribosome rearrangement
Map datareconstruction of codon-recognition / GTPase activation state of 80S ribosome
Sample
  • Sample: Codon recognition /GTPase activated state of mammalian 80S ribosome
  • Complex: Re-associated 80S
  • RNA: transfer RNA
  • RNA: transfer RNA
  • RNA: transfer RNA
  • RNA: messenger RNA
  • Protein or peptide: elongation factor 1A
Keywordstranslation / mammalian 80S ribosome / elongation cycle / tRNA selection / eukaryotic ternary complex / elongation factor eEF1A / cryo-electron microscopy
Function / homology
Function and homology information


regulation of D-erythro-sphingosine kinase activity / guanyl nucleotide binding / positive regulation by host of viral genome replication / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / cortical actin cytoskeleton / SARS-CoV-1 modulates host translation machinery / Protein hydroxylation / Peptide chain elongation ...regulation of D-erythro-sphingosine kinase activity / guanyl nucleotide binding / positive regulation by host of viral genome replication / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / cortical actin cytoskeleton / SARS-CoV-1 modulates host translation machinery / Protein hydroxylation / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / rough endoplasmic reticulum / stress granule assembly / translation elongation factor activity / cellular response to epidermal growth factor stimulus / small-subunit processome / cytosolic ribosome / maintenance of translational fidelity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosomal small subunit biogenesis / ruffle membrane / Regulation of expression of SLITs and ROBOs / cytosolic small ribosomal subunit / cytoplasmic translation / SARS-CoV-2 modulates host translation machinery / tRNA binding / molecular adaptor activity / ribosome / structural constituent of ribosome / translation / GTPase activity / synapse / GTP binding / nucleolus / protein kinase binding / endoplasmic reticulum / RNA binding / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Translation elongation factor EF1A, eukaryotic/archaeal / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein S23, eukaryotic/archaeal / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain ...Translation elongation factor EF1A, eukaryotic/archaeal / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein S23, eukaryotic/archaeal / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Small GTP-binding protein domain / Ribosomal protein S12 signature. / Translation protein, beta-barrel domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Small ribosomal subunit protein uS12 / Elongation factor 1-alpha 1 / Elongation factor 1-alpha
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.9 Å
AuthorsBudkevich TV / Giesebrecht J / Behrmann E / Loerke J / Ramrath D / Mielke T / Ismer J / Hildebrand P / Tung C-S / Nierhaus KH ...Budkevich TV / Giesebrecht J / Behrmann E / Loerke J / Ramrath D / Mielke T / Ismer J / Hildebrand P / Tung C-S / Nierhaus KH / Sanbonmatsu KY / Spahn CMT
CitationJournal: Cell / Year: 2014
Title: Regulation of the mammalian elongation cycle by subunit rolling: a eukaryotic-specific ribosome rearrangement.
Authors: Tatyana V Budkevich / Jan Giesebrecht / Elmar Behrmann / Justus Loerke / David J F Ramrath / Thorsten Mielke / Jochen Ismer / Peter W Hildebrand / Chang-Shung Tung / Knud H Nierhaus / ...Authors: Tatyana V Budkevich / Jan Giesebrecht / Elmar Behrmann / Justus Loerke / David J F Ramrath / Thorsten Mielke / Jochen Ismer / Peter W Hildebrand / Chang-Shung Tung / Knud H Nierhaus / Karissa Y Sanbonmatsu / Christian M T Spahn /
Abstract: The extent to which bacterial ribosomes and the significantly larger eukaryotic ribosomes share the same mechanisms of ribosomal elongation is unknown. Here, we present subnanometer resolution ...The extent to which bacterial ribosomes and the significantly larger eukaryotic ribosomes share the same mechanisms of ribosomal elongation is unknown. Here, we present subnanometer resolution cryoelectron microscopy maps of the mammalian 80S ribosome in the posttranslocational state and in complex with the eukaryotic eEF1A⋅Val-tRNA⋅GMPPNP ternary complex, revealing significant differences in the elongation mechanism between bacteria and mammals. Surprisingly, and in contrast to bacterial ribosomes, a rotation of the small subunit around its long axis and orthogonal to the well-known intersubunit rotation distinguishes the posttranslocational state from the classical pretranslocational state ribosome. We term this motion "subunit rolling." Correspondingly, a mammalian decoding complex visualized in substates before and after codon recognition reveals structural distinctions from the bacterial system. These findings suggest how codon recognition leads to GTPase activation in the mammalian system and demonstrate that in mammalia subunit rolling occurs during tRNA selection.
History
DepositionApr 2, 2014-
Header (metadata) releaseApr 16, 2014-
Map releaseJul 9, 2014-
UpdateJul 16, 2014-
Current statusJul 16, 2014Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-4cxh
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4cxh
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2624_500...

Downloads & links

-
Map

FileDownload / File: emd_2624.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationreconstruction of codon-recognition / GTPase activation state of 80S ribosome
Voxel sizeX=Y=Z: 1.26 Å
Density
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-5.81728458 - 14.470520970000001
Average (Standard dev.)0.22896801 (±0.95430303)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin180180180
Dimensions360360360
Spacing360360360
CellA=B=C: 453.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.261.261.26
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z453.600453.600453.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS180180180
NC/NR/NS360360360
D min/max/mean-5.81714.4710.229

-
Supplemental data

-
Sample components

-
Entire : Codon recognition /GTPase activated state of mammalian 80S ribosome

EntireName: Codon recognition /GTPase activated state of mammalian 80S ribosome
Components
  • Sample: Codon recognition /GTPase activated state of mammalian 80S ribosome
  • Complex: Re-associated 80S
  • RNA: transfer RNA
  • RNA: transfer RNA
  • RNA: transfer RNA
  • RNA: messenger RNA
  • Protein or peptide: elongation factor 1A

-
Supramolecule #1000: Codon recognition /GTPase activated state of mammalian 80S ribosome

SupramoleculeName: Codon recognition /GTPase activated state of mammalian 80S ribosome
type: sample / ID: 1000
Details: 80S were re-associated and the sample was assembled in vitro from individual components
Oligomeric state: one 80S binds three tRNAs, one elongation factor eEF1A and one mRNA
Number unique components: 6
Molecular weightTheoretical: 4.5 MDa

-
Supramolecule #1: Re-associated 80S

SupramoleculeName: Re-associated 80S / type: complex / ID: 1 / Name.synonym: 80S ribosome / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Liver
Molecular weightTheoretical: 4.5 MDa

-
Macromolecule #1: transfer RNA

MacromoleculeName: transfer RNA / type: rna / ID: 1 / Name.synonym: tRNA / Details: tRNAPhe / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit
Molecular weightTheoretical: 25 KDa

-
Macromolecule #2: transfer RNA

MacromoleculeName: transfer RNA / type: rna / ID: 2 / Name.synonym: tRNA / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit
Molecular weightTheoretical: 25 KDa

-
Macromolecule #3: transfer RNA

MacromoleculeName: transfer RNA / type: rna / ID: 3 / Name.synonym: tRNA / Details: Val-tRNAVal / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit
Molecular weightTheoretical: 25 KDa

-
Macromolecule #5: messenger RNA

MacromoleculeName: messenger RNA / type: rna / ID: 5 / Name.synonym: mRNA / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Strain: XL-1 blue
Molecular weightTheoretical: 15 KDa
SequenceString:
GGGAAAAGAA AAGAAAAGAA AAUGUUCGUU AAAGAAAAGA AAAGAAAU

-
Macromolecule #4: elongation factor 1A

MacromoleculeName: elongation factor 1A / type: protein_or_peptide / ID: 4 / Name.synonym: eEF1A / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Liver
Molecular weightTheoretical: 50 KDa
SequenceUniProtKB: Elongation factor 1-alpha 1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.3 mg/mL
BufferpH: 7.5
Details: 20 mM Hepes, 5 mM MgCl2, 100 mM NH4Cl, 6 mM beta-mercaptoethanol, 0.8 mM spermidine, 0.6 mM spermine
GridDetails: Quantifoil grids with additional continuous carbon support.
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Instrument: FEI VITROBOT MARK II / Method: blot for 2/4 sec before plunging

-
Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 65520 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 39000
Sample stageSpecimen holder: Nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 77 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification
Detailsminimal dose system
DateSep 22, 2008
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Number real images: 230 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: defocus group
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.9 Å / Resolution method: OTHER / Software - Name: Spider, Sparx / Number images used: 52686
DetailsThe particles were selected using SIGNATURE and processed using SPIDER and SPARX.

-
Atomic model buiding 1

Initial modelPDB ID:

3vmf


Chain - Chain ID: A
SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation
Output model

PDB-4cxh:
Regulation of the mammalian elongation cycle by 40S subunit rolling: a eukaryotic-specific ribosome rearrangement

-
Atomic model buiding 2

Initial modelPDB ID:

2xqd
PDB Unreleased entry


Chain - Chain ID: Y
SoftwareName: Chimera, Coot
DetailsAcceptor stem loop (2XQD) and tRNA body (1TTT) (cutting points 26-27, 43-44) were docked separately as rigid bodies. Cutting points were restored using Coot.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation
Output model

PDB-4cxh:
Regulation of the mammalian elongation cycle by 40S subunit rolling: a eukaryotic-specific ribosome rearrangement

-
Atomic model buiding 3

Initial modelPDB ID:

1ttt


Chain - Chain ID: D
SoftwareName: Chimera, Coot
DetailsAcceptor stem loop (2XQD) and tRNA body (1TTT) (cutting points 26-27, 43-44) were docked separately as rigid bodies. Cutting points were restored using Coot.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation
Output model

PDB-4cxh:
Regulation of the mammalian elongation cycle by 40S subunit rolling: a eukaryotic-specific ribosome rearrangement

+
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