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- EMDB-5513: Structure of late pre-60S ribosomal subunits with nuclear export ... -

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Basic information

Entry
Database: EMDB / ID: EMD-5513
TitleStructure of late pre-60S ribosomal subunits with nuclear export factor Arx1 bound at the peptide exit tunnel
Map dataReconstruction of pre-60S ribosomal subunits with nuclear export factor Arx1 bound at the peptide exit tunnel
Sample
  • Sample: pre-60S particle
  • Complex: Pre-60S particle
  • Protein or peptide: Proliferation-associated protein 2G4
Keywordsribosome pre-ribosome pre-60S factors
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 / ribosomal subunit export from nucleus / ribosomal large subunit binding / preribosome, large subunit precursor / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / translation initiation factor activity / assembly of large subunit precursor of preribosome ...maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / ribosomal subunit export from nucleus / ribosomal large subunit binding / preribosome, large subunit precursor / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / translation initiation factor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / positive regulation of cell differentiation / rRNA processing / transcription corepressor activity / azurophil granule lumen / regulation of translation / nucleic acid binding / ribonucleoprotein complex / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / Neutrophil degranulation / nucleolus / negative regulation of apoptotic process / RNA binding / extracellular exosome / extracellular region / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
PA2G4 family / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like ...PA2G4 family / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Eukaryotic translation initiation factor 6 / Proliferation-associated protein 2G4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.9 Å
AuthorsBradatsch B / Leidig C / Granneman S / Gnaedig M / Tollervey D / Boettcher B / Beckmann R / Hurt E
CitationJournal: Nat Struct Mol Biol / Year: 2012
Title: Structure of the pre-60S ribosomal subunit with nuclear export factor Arx1 bound at the exit tunnel.
Authors: Bettina Bradatsch / Christoph Leidig / Sander Granneman / Marén Gnädig / David Tollervey / Bettina Böttcher / Roland Beckmann / Ed Hurt /
Abstract: Preribosomal particles evolve in the nucleus through transient interaction with biogenesis factors before export to the cytoplasm. Here, we report the architecture of the late pre-60S particle, ...Preribosomal particles evolve in the nucleus through transient interaction with biogenesis factors before export to the cytoplasm. Here, we report the architecture of the late pre-60S particle, purified from Saccharomyces cerevisiae, through Arx1, a nuclear export factor with structural homology to methionine aminopeptidases, or its binding partner Alb1. Cryo-EM reconstruction of the Arx1 particle at 11.9-Å resolution reveals regions of extra density on the pre-60S particle attributed to associated biogenesis factors, confirming the immature state of the nascent subunit. One of these densities could be unambiguously assigned to Arx1. Immunoelectron microscopy and UV cross-linking localize Arx1 close to the ribosomal exit tunnel, in direct contact with ES27, a highly dynamic eukaryotic rRNA expansion segment. The binding of Arx1 at the exit tunnel may position this export factor to prevent premature recruitment of ribosome-associated factors active during translation.
History
DepositionOct 4, 2012-
Header (metadata) releaseOct 31, 2012-
Map releaseNov 7, 2012-
UpdateNov 28, 2012-
Current statusNov 28, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.48
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.48
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j2i
  • Surface level: 0.48
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j2i
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5513.png

Downloads & links

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Map

FileDownload / File: emd_5513.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of pre-60S ribosomal subunits with nuclear export factor Arx1 bound at the peptide exit tunnel
Voxel sizeX=Y=Z: 1.2375 Å
Density
Contour LevelBy EMDB: 0.5 / Movie #1: 0.48
Minimum - Maximum-1.01602316 - 3.0163188
Average (Standard dev.)-0.00301202 (±0.21357282)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-184-184-183
Dimensions368368368
Spacing368368368
CellA=B=C: 455.4 Å
α=β=γ: 90.0 °

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-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS-184-184-183
NC/NR/NS368368368
D min/max/mean-1.0163.016-0.003

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Supplemental data

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Sample components

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Entire : pre-60S particle

EntireName: pre-60S particle
Components
  • Sample: pre-60S particle
  • Complex: Pre-60S particle
  • Protein or peptide: Proliferation-associated protein 2G4

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Supramolecule #1000: pre-60S particle

SupramoleculeName: pre-60S particle / type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 1.3 MDa / Theoretical: 1.3 MDa

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Supramolecule #1: Pre-60S particle

SupramoleculeName: Pre-60S particle / type: complex / ID: 1 / Name.synonym: pre-60S / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-eukaryote: LSU 60S
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: yeast

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Macromolecule #1: Proliferation-associated protein 2G4

MacromoleculeName: Proliferation-associated protein 2G4 / type: protein_or_peptide / ID: 1 / Name.synonym: Ebp1 / Number of copies: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: human

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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

BufferpH: 7
Details: 50 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1.5 mM or 5 mM MgCl2, 0.075% (v/v) NP-40
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 95000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateApr 6, 2012
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Average electron dose: 20 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Subvolumes
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Signature, Spider, Chimera / Number images used: 100000
DetailsThe particles were selected using an automatic selection program

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