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- EMDB-1285: Structure of the ribosome-bound cricket paralysis virus IRES RNA. -

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Basic information

Entry
Database: EMDB / ID: EMD-1285
TitleStructure of the ribosome-bound cricket paralysis virus IRES RNA.
Map dataComplex between the yeast 80S ribosome and the cricket paralysis virus IRES
Sample
  • Sample: yeast 80S ribosome in complex with the CrPV IRES RNA
  • Complex: yeast 80S ribosome
  • RNA: CrPV IRES
Function / homology
Function and homology information


Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus ...Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / 90S preribosome / regulation of translational fidelity / ribosomal subunit export from nucleus / maturation of LSU-rRNA / maturation of SSU-rRNA / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein S5/S7, eukaryotic/archaeal / : / Ribosomal protein L5, conserved site ...Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein S5/S7, eukaryotic/archaeal / : / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e
Similarity search - Domain/homology
Large ribosomal subunit protein uL1A / Small ribosomal subunit protein uS7 / 60S ribosomal protein L1-B / Large ribosomal subunit protein uL5B
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsSchuler M / Connell SR / Lescoute A / Giesebrecht J / Dabrowski M / Schroeer B / Mielke T / Penczek PA / Westhof E / Spahn CM
CitationJournal: Nat Struct Mol Biol / Year: 2006
Title: Structure of the ribosome-bound cricket paralysis virus IRES RNA.
Authors: Martin Schüler / Sean R Connell / Aurelie Lescoute / Jan Giesebrecht / Marylena Dabrowski / Birgit Schroeer / Thorsten Mielke / Pawel A Penczek / Eric Westhof / Christian M T Spahn /
Abstract: Internal ribosome entry sites (IRESs) facilitate an alternative, end-independent pathway of translation initiation. A particular family of dicistroviral IRESs can assemble elongation-competent 80S ...Internal ribosome entry sites (IRESs) facilitate an alternative, end-independent pathway of translation initiation. A particular family of dicistroviral IRESs can assemble elongation-competent 80S ribosomal complexes in the absence of canonical initiation factors and initiator transfer RNA. We present here a cryo-EM reconstruction of a dicistroviral IRES bound to the 80S ribosome. The resolution of the cryo-EM reconstruction, in the subnanometer range, allowed the molecular structure of the complete IRES in its active, ribosome-bound state to be solved. The structure, harboring three pseudoknot-containing domains, each with a specific functional role, shows how defined elements of the IRES emerge from a compactly folded core and interact with the key ribosomal components that form the A, P and E sites, where tRNAs normally bind. Our results exemplify the molecular strategy for recruitment of an IRES and reveal the dynamic features necessary for internal initiation.
History
DepositionOct 31, 2006-
Header (metadata) releaseOct 31, 2006-
Map releaseOct 31, 2007-
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: 1.2
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 1.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2noq
  • Surface level: 1.2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2noq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1285.gif

Downloads & links

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Map

FileDownload / File: emd_1285.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComplex between the yeast 80S ribosome and the cricket paralysis virus IRES
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 300 pix.
= 366. Å		1.22 Å/pix.
x 300 pix.
= 366. Å		1.22 Å/pix.
x 300 pix.
= 366. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.22 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 2.76 / Movie #1: 1.2
Minimum - Maximum-6.03604 - 12.044600000000001
Average (Standard dev.)0.0102696 (±1.28183)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 366 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.221.221.22
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z366.000366.000366.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-6.03612.0450.010

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Supplemental data

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Sample components

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Entire : yeast 80S ribosome in complex with the CrPV IRES RNA

EntireName: yeast 80S ribosome in complex with the CrPV IRES RNA
Components
  • Sample: yeast 80S ribosome in complex with the CrPV IRES RNA
  • Complex: yeast 80S ribosome
  • RNA: CrPV IRES

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Supramolecule #1000: yeast 80S ribosome in complex with the CrPV IRES RNA

SupramoleculeName: yeast 80S ribosome in complex with the CrPV IRES RNA / type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: yeast 80S ribosome

SupramoleculeName: yeast 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: CrPV IRES

MacromoleculeName: CrPV IRES / type: rna / ID: 1 / Classification: OTHER / Structure: DOUBLE HELIX / Synthetic?: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker

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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 / Details: Vitrification instrument: FEI Vitrobot

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 4.7 µm / Number real images: 341 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.9 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 39000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Defocus groups
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 73313

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