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- EMDB-1067: Domain movements of elongation factor eEF2 and the eukaryotic 80S... -

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Basic information

Entry
Database: EMDB / ID: EMD-1067
TitleDomain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
Map datamap
Sample
  • Sample: Ribosomal 80S-eEF2-sordarin complex from S. cerevisiae
  • Complex: 80S ribosome
  • Protein or peptide: eEF2
Function / homology
Function and homology information


: / Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / Protein hydroxylation ...: / Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / nonfunctional rRNA decay / response to cycloheximide / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of translational frameshifting / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 90S preribosome / translation elongation factor activity / ribosomal subunit export from nucleus / regulation of translational fidelity / 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) / translational termination / maturation of LSU-rRNA / ribosomal small subunit export from nucleus / translation regulator activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled ribosome / Neutrophil degranulation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / protein kinase C binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / translational initiation / small-subunit processome / maintenance of translational fidelity / cytoplasmic stress granule / rRNA processing / large ribosomal subunit / protein-folding chaperone binding / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / G protein-coupled receptor signaling pathway / translation / ribonucleoprotein complex / negative regulation of gene expression / response to antibiotic / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / : ...Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / : / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L44e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / : / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein S3, eukaryotic/archaeal / Elongation factor Tu domain 2 / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein S19A/S15e / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / 60S ribosomal protein L19 / Ribosomal protein L7A/L8 / 60S ribosomal protein L35 / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L18e / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal protein L31e, conserved site / Ribosomal L30 N-terminal domain / Ribosomal protein L31e signature. / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2. / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L15e, conserved site / Ribosomal protein L15e signature. / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L21e / Ribosomal protein L21e signature. / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e
Similarity search - Domain/homology
Small ribosomal subunit protein uS4A / 60S ribosomal protein L42-A / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL24A / 60S ribosomal protein L23-B / Large ribosomal subunit protein uL23 / 40S ribosomal protein S22-A / 60S ribosomal protein L31-B / 60S ribosomal protein L19-A / 60S ribosomal protein L2-A ...Small ribosomal subunit protein uS4A / 60S ribosomal protein L42-A / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL24A / 60S ribosomal protein L23-B / Large ribosomal subunit protein uL23 / 40S ribosomal protein S22-A / 60S ribosomal protein L31-B / 60S ribosomal protein L19-A / 60S ribosomal protein L2-A / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL15A / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / 60S ribosomal protein L11-B / 60S ribosomal protein L18-A / Large ribosomal subunit protein eL31B / Large ribosomal subunit protein eL43B / Large ribosomal subunit protein eL42B / Small ribosomal subunit protein uS12B / Large ribosomal subunit protein uL14B / Large ribosomal subunit protein uL1A / Large ribosomal subunit protein uL2B / Small ribosomal subunit protein uS17B / Large ribosomal subunit protein eL18B / Small ribosomal subunit protein uS9B / Large ribosomal subunit protein uL11A / Small ribosomal subunit protein uS13B / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL29A / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / 60S ribosomal protein L12-A / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / 40S ribosomal protein S11-B / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13A / Elongation factor 2 / 40S ribosomal protein S23-A / Small ribosomal subunit protein uS2A / 40S ribosomal protein S18-A / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS10 / 60S ribosomal protein L35-A / 40S ribosomal protein S16-B / Small ribosomal subunit protein uS14B / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein uL4B / 60S ribosomal protein L43-A / 60S ribosomal protein L1-B / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL21A / Large ribosomal subunit protein uL5B / Small ribosomal subunit protein uS8B
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.7 Å
AuthorsSpahn CM / Frank J
CitationJournal: EMBO J / Year: 2004
Title: Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
Authors: Christian M T Spahn / Maria G Gomez-Lorenzo / Robert A Grassucci / Rene Jørgensen / Gregers R Andersen / Roland Beckmann / Pawel A Penczek / Juan P G Ballesta / Joachim Frank /
Abstract: An 11.7-A-resolution cryo-EM map of the yeast 80S.eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and ...An 11.7-A-resolution cryo-EM map of the yeast 80S.eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and the 80S ribosome, including a rearrangement of the functionally important ribosomal intersubunit bridges. Sordarin positions domain III of eEF2 so that it can interact with the sarcin-ricin loop of 25S rRNA and protein rpS23 (S12p). This particular conformation explains the inhibitory action of sordarin and suggests that eEF2 is stalled on the 80S ribosome in a conformation that has similarities with the GTPase activation state. A ratchet-like subunit rearrangement (RSR) occurs in the 80S.eEF2.sordarin complex that, in contrast to Escherichia coli 70S ribosomes, is also present in vacant 80S ribosomes. A model is suggested, according to which the RSR is part of a mechanism for moving the tRNAs during the translocation reaction.
History
DepositionJan 5, 2004-
Header (metadata) releaseJan 6, 2004-
Map releaseJan 6, 2005-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0003
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0003
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-1trj, PDB-4v4b
  • Surface level: 0.0003
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1trj
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1067.gif

Downloads & links

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Map

FileDownload / File: emd_1067.map.gz / Format: CCP4 / Size: 7.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.93 Å/pix.
x 125 pix.
= 366.25 Å		2.93 Å/pix.
x 125 pix.
= 366.25 Å		2.93 Å/pix.
x 125 pix.
= 366.25 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.93 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.000477 / Movie #1: 0.0003
Minimum - Maximum-0.00084646 - 0.00169185
Average (Standard dev.)0.0000169393 (±0.00020054)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-62-62-62
Dimensions125125125
Spacing125125125
CellA=B=C: 366.25 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.932.932.93
M x/y/z125125125
origin x/y/z0.0000.0000.000
length x/y/z366.250366.250366.250
α/β/γ90.00090.00090.000
start NX/NY/NZ0052
NX/NY/NZ12812855
MAP C/R/S123
start NC/NR/NS-62-62-62
NC/NR/NS125125125
D min/max/mean-0.0010.0020.000

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Supplemental data

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Sample components

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Entire : Ribosomal 80S-eEF2-sordarin complex from S. cerevisiae

EntireName: Ribosomal 80S-eEF2-sordarin complex from S. cerevisiae
Components
  • Sample: Ribosomal 80S-eEF2-sordarin complex from S. cerevisiae
  • Complex: 80S ribosome
  • Protein or peptide: eEF2

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Supramolecule #1000: Ribosomal 80S-eEF2-sordarin complex from S. cerevisiae

SupramoleculeName: Ribosomal 80S-eEF2-sordarin complex from S. cerevisiae
type: sample / ID: 1000 / Number unique components: 2
Molecular weightTheoretical: 3.2 MDa

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Supramolecule #1: 80S ribosome

SupramoleculeName: 80S ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast

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Macromolecule #1: eEF2

MacromoleculeName: eEF2 / type: protein_or_peptide / ID: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 93 K
Alignment procedureLegacy - Astigmatism: 100,000 X magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Number real images: 86 / Average electron dose: 15 e/Å2 / Bits/pixel: 12
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 50000
Sample stageSpecimen holder: Oxford, cryo-transfer 3500 / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: defocus group volumes
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER

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