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- EMDB-5943: Cryo-EM Map of a yeast ribosome bound to the TSV IRES (Class I) -

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Basic information

Entry
Database: EMDB / ID: EMD-5943
TitleCryo-EM Map of a yeast ribosome bound to the TSV IRES (Class I)
Map dataReconstruction of a yeast 80S ribosome bound with the TSV IRES
Sample
  • Sample: Saccharomyces cerevisiae 80S ribosome bound with TSV IRES
  • Complex: Saccharomyces cerevisiae 80S ribosome
  • RNA: Internal Ribosome Entry Site
KeywordsTranslation Initiation / Internal Ribosome Entry Site
Function / homology
Function and homology information


maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / GDP-dissociation inhibitor activity / mTORC1-mediated signalling / ribosome-associated ubiquitin-dependent protein catabolic process / Protein hydroxylation ...maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / GDP-dissociation inhibitor activity / mTORC1-mediated signalling / ribosome-associated ubiquitin-dependent protein catabolic process / Protein hydroxylation / : / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / response to cycloheximide / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / 90S preribosome / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / protein-RNA complex assembly / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 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) / regulation of translational fidelity / positive regulation of protein kinase activity / ribosomal small subunit export from nucleus / translation regulator activity / translational termination / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to amino acid starvation / ribosome assembly / ribosomal large subunit biogenesis / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / macroautophagy / modification-dependent protein catabolic process / protein tag activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / cytoplasmic stress granule / small ribosomal subunit rRNA binding / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / small ribosomal subunit / cytoplasmic translation / negative regulation of translation / ribosome / rRNA binding / protein ubiquitination / structural constituent of ribosome / translation / G protein-coupled receptor signaling pathway / positive regulation of protein phosphorylation / response to antibiotic / negative regulation of gene expression / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Ribosomal protein S26e signature. / : / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. ...: / Ribosomal protein S26e signature. / : / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal L29e protein family / Ribosomal protein S10, eukaryotic/archaeal / 40S Ribosomal protein S10 / S27a-like superfamily / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Plectin/S10, N-terminal / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Plectin/S10 domain / Ribosomal protein L1, conserved site / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L1 signature. / Ribosomal protein S27a / : / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S8e subdomain, eukaryotes / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal L40e family / Ribosomal protein L1 / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L44e signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L40e superfamily / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e / Ribosomal protein S7e signature. / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S27e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein L44e / Ribosomal protein L19/L19e conserved site / Ribosomal protein L44 / Ribosomal protein L19e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L5 eukaryotic, C-terminal / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L18 C-terminal region / Ribosomal protein L34e signature. / Ribosomal protein L6e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L30e signature 1. / Ribosomal S24e conserved site / Ribosomal protein S24e signature.
Similarity search - Domain/homology
Small ribosomal subunit protein uS4A / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS17A / Large ribosomal subunit protein eL24A / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A ...Small ribosomal subunit protein uS4A / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS17A / Large ribosomal subunit protein eL24A / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL22A / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS15 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein eS21A / Small ribosomal subunit protein uS8A / Large ribosomal subunit protein uL5A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL31A / Ubiquitin-ribosomal protein eL40A fusion protein / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL43A / Large ribosomal subunit protein eL42A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein uL1A / Large ribosomal subunit protein uL2A / Small ribosomal subunit protein uS17A / Large ribosomal subunit protein eL18A / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS13A / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein uL29A / Small ribosomal subunit protein eS32A / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13A / Small ribosomal subunit protein eS7A / Small ribosomal subunit protein uS2A / Small ribosomal subunit protein eS1A / Small ribosomal subunit protein eS27A / Large ribosomal subunit protein eL14A / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS26A / Small ribosomal subunit protein uS14A / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL34A / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL6A / Large ribosomal subunit protein eL21A / Small ribosomal subunit protein eS10A / Large ribosomal subunit protein eL13A / Small ribosomal subunit protein eS25A / Small ribosomal subunit protein eS28A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Taura syndrome virus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsKoh CS / Brilot AF / Grigorieff N / Korostelev AA
CitationJournal: Proc Natl Acad Sci U S A / Year: 2014
Title: Taura syndrome virus IRES initiates translation by binding its tRNA-mRNA-like structural element in the ribosomal decoding center.
Authors: Cha San Koh / Axel F Brilot / Nikolaus Grigorieff / Andrei A Korostelev /
Abstract: In cap-dependent translation initiation, the open reading frame (ORF) of mRNA is established by the placement of the AUG start codon and initiator tRNA in the ribosomal peptidyl (P) site. Internal ...In cap-dependent translation initiation, the open reading frame (ORF) of mRNA is established by the placement of the AUG start codon and initiator tRNA in the ribosomal peptidyl (P) site. Internal ribosome entry sites (IRESs) promote translation of mRNAs in a cap-independent manner. We report two structures of the ribosome-bound Taura syndrome virus (TSV) IRES belonging to the family of Dicistroviridae intergenic IRESs. Intersubunit rotational states differ in these structures, suggesting that ribosome dynamics play a role in IRES translocation. Pseudoknot I of the IRES occupies the ribosomal decoding center at the aminoacyl (A) site in a manner resembling that of the tRNA anticodon-mRNA codon. The structures reveal that the TSV IRES initiates translation by a previously unseen mechanism, which is conceptually distinct from initiator tRNA-dependent mechanisms. Specifically, the ORF of the IRES-driven mRNA is established by the placement of the preceding tRNA-mRNA-like structure in the A site, whereas the 40S P site remains unoccupied during this initial step.
History
DepositionApr 9, 2014-
Header (metadata) releaseMay 28, 2014-
Map releaseJun 11, 2014-
UpdateOct 7, 2015-
Current statusOct 7, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.815
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.815
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j6y
  • Surface level: 0.815
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5943.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of a yeast 80S ribosome bound with the TSV IRES
Voxel sizeX=Y=Z: 1.0595 Å
Density
Contour LevelBy AUTHOR: 0.815 / Movie #1: 0.815
Minimum - Maximum-1.66221809 - 4.06740475
Average (Standard dev.)0.02754904 (±0.28348586)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 444.99 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.05951.05951.0595
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z444.990444.990444.990
α/β/γ90.00090.00090.000
start NX/NY/NZ-800-4
NX/NY/NZ1611358
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-1.6624.0670.028

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Supplemental data

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Sample components

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Entire : Saccharomyces cerevisiae 80S ribosome bound with TSV IRES

EntireName: Saccharomyces cerevisiae 80S ribosome bound with TSV IRES
Components
  • Sample: Saccharomyces cerevisiae 80S ribosome bound with TSV IRES
  • Complex: Saccharomyces cerevisiae 80S ribosome
  • RNA: Internal Ribosome Entry Site

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Supramolecule #1000: Saccharomyces cerevisiae 80S ribosome bound with TSV IRES

SupramoleculeName: Saccharomyces cerevisiae 80S ribosome bound with TSV IRES
type: sample / ID: 1000 / Number unique components: 2
Molecular weightExperimental: 3.5 MDa / Theoretical: 3.5 MDa

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Supramolecule #1: Saccharomyces cerevisiae 80S ribosome

SupramoleculeName: Saccharomyces cerevisiae 80S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303 / synonym: Yeast
Molecular weightExperimental: 3.4 MDa / Theoretical: 3.4 MDa

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Macromolecule #1: Internal Ribosome Entry Site

MacromoleculeName: Internal Ribosome Entry Site / type: rna / ID: 1 / Name.synonym: IRES / Classification: OTHER / Structure: DOUBLE HELIX / Synthetic?: Yes
Source (natural)Organism: Taura syndrome virus
Molecular weightExperimental: 80 KDa / Theoretical: 80 KDa
SequenceString: UAGCACCACC CGAUCGUAAA CUCCAUGUAU UGGUUACCCA UCUGCAUCGA AAACUCUCCG AACACUAGGU GCAGUAAGGC UUUCAUGGAG UGGUUUGCUA UUUAGCGUAC GUGUACCAUA GGCAGCCCCA AAAACACGUG UGAGGAGAAA GUCCCAGUCA CUUUGGGCAA ...String:
UAGCACCACC CGAUCGUAAA CUCCAUGUAU UGGUUACCCA UCUGCAUCGA AAACUCUCCG AACACUAGGU GCAGUAAGGC UUUCAUGGAG UGGUUUGCUA UUUAGCGUAC GUGUACCAUA GGCAGCCCCA AAAACACGUG UGAGGAGAAA GUCCCAGUCA CUUUGGGCAA AGUAGACAGC CGCGCUUGCG UGGUGGGACU UAAUUAAUGC CUGCUAACCC AGUUGAAAUU GAUAAUUUUG AUACAACAAC

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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

Concentration1.044 mg/mL
BufferpH: 7.5
Details: 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/ul RNasin
GridDetails: C-flat 1.2-1.3 400C
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK II / Method: Fresh glow discharge, 7 second blot

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 132138 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal defocus max: 6.53 µm / Nominal defocus min: 1.15 µm / Nominal magnification: 133333
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Alignment procedureLegacy - Astigmatism: Corrected using FEI software bundled with Titan Krios/Cs Corrector.
DateDec 26, 2012
Image recordingCategory: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Digitization - Sampling interval: 14.0 µm / Number real images: 11498 / Average electron dose: 30 e/Å2 / Bits/pixel: 32
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: CTFFIND3, FREALIGN per micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: OTHER / Software - Name: EMAN2, IMAGIC, FREALIGN, RSAMPLE, CTFFIND3 / Number images used: 51373

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