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- EMDB-1705: Mechanism of eIF6s anti-association activity -

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Basic information

Entry
Database: EMDB / ID: EMD-1705
TitleMechanism of eIF6s anti-association activity
Map data60S-eIF6 complex from S. cerevisiae
Sample
  • Sample: 60S-eIF6 complex
  • Complex: 60S
  • Protein or peptide: EUKARYOTIC TRANSLATION INITIATION FACTOR 6
Keywords60S / ribosome / eIF6
Function / homology
Function and homology information


maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / 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 ...maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / 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 / translational elongation / ribosomal subunit export from nucleus / maturation of LSU-rRNA / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / cytosolic ribosome assembly / translational initiation / rRNA processing / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / structural constituent of ribosome / mRNA binding / nucleolus / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. ...Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. / Ribosomal protein L14p/L23e / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e
Similarity search - Domain/homology
Large ribosomal subunit protein eL24A / 60S ribosomal protein L23-B / Large ribosomal subunit protein uL14A / Eukaryotic translation initiation factor 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.8 Å
AuthorsGartmann M / Blau M / Armache J-P / Mielke T / Topf M / Beckmann R
CitationJournal: J Biol Chem / Year: 2010
Title: Mechanism of eIF6-mediated inhibition of ribosomal subunit joining.
Authors: Marco Gartmann / Michael Blau / Jean-Paul Armache / Thorsten Mielke / Maya Topf / Roland Beckmann /
Abstract: During the process of ribosomal assembly, the essential eukaryotic translation initiation factor 6 (eIF6) is known to act as a ribosomal anti-association factor. However, a molecular understanding of ...During the process of ribosomal assembly, the essential eukaryotic translation initiation factor 6 (eIF6) is known to act as a ribosomal anti-association factor. However, a molecular understanding of the anti-association activity of eIF6 is still missing. Here we present the cryo-electron microscopy reconstruction of a complex of the large ribosomal subunit with eukaryotic eIF6 from Saccharomyces cerevisiae. The structure reveals that the eIF6 binding site involves mainly rpL23 (L14p in Escherichia coli). Based on our structural data, we propose that the mechanism of the anti-association activity of eIF6 is based on steric hindrance of intersubunit bridge formation around the dynamic bridge B6.
History
DepositionMar 1, 2010-
Header (metadata) releaseApr 26, 2011-
Map releaseApr 26, 2011-
UpdateApr 16, 2014-
Current statusApr 16, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2x7n
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2x7n
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

em1705.png

Downloads & links

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Map

FileDownload / File: emd_1705.map.gz / Format: CCP4 / Size: 6.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation60S-eIF6 complex from S. cerevisiae
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
3.71 Å/pix.
x 122 pix.
= 452.62 Å		3.71 Å/pix.
x 122 pix.
= 452.62 Å		3.71 Å/pix.
x 122 pix.
= 452.62 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.024 / Movie #1: 0.024
Minimum - Maximum-0.0433532 - 0.129382
Average (Standard dev.)0.00042245 (±0.00940148)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-61-61-60
Dimensions122122122
Spacing122122122
CellA=B=C: 452.62 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.713.713.71
M x/y/z122122122
origin x/y/z0.0000.0000.000
length x/y/z452.620452.620452.620
α/β/γ90.00090.00090.000
start NX/NY/NZ-61-61-60
NX/NY/NZ122122122
MAP C/R/S213
start NC/NR/NS-61-61-60
NC/NR/NS122122122
D min/max/mean-0.0430.1290.000

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Supplemental data

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Sample components

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Entire : 60S-eIF6 complex

EntireName: 60S-eIF6 complex
Components
  • Sample: 60S-eIF6 complex
  • Complex: 60S
  • Protein or peptide: EUKARYOTIC TRANSLATION INITIATION FACTOR 6

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Supramolecule #1000: 60S-eIF6 complex

SupramoleculeName: 60S-eIF6 complex / type: sample / ID: 1000
Details: Reconstituted complex of 60S subunits with eIF6 in vitreous ice
Oligomeric state: Heterodimer / Number unique components: 2

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Supramolecule #1: 60S

SupramoleculeName: 60S / type: complex / ID: 1 / Name.synonym: 60S ribosomal subunit / Details: 60S subunit, contains rpL23, rpL24 and SRL. / Ribosome-details: ribosome-eukaryote: LSU 60S

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Macromolecule #1: EUKARYOTIC TRANSLATION INITIATION FACTOR 6

MacromoleculeName: EUKARYOTIC TRANSLATION INITIATION FACTOR 6 / type: protein_or_peptide / ID: 1 / Name.synonym: EIF-6 / Details: Residues 1-224 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightTheoretical: 25 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer'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 / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureMin: 95 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38900 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal magnification: 39000
Sample stageSpecimen holder: FEI Polara cartridge system / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Defocus group volumes
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 11.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider

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Atomic model buiding 1

Initial modelPDB ID:

1g62


Chain - Chain ID: A
SoftwareName: Flex-EM
DetailsPDBEntryID_givenInChain.
RefinementSpace: REAL
Output model

PDB-2x7n:
Mechanism of eIF6s anti-association activity

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