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- EMDB-2451: Cryo-EM structure of the CSFV IRES in complex with eIF3, small ri... -

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Basic information

Entry
Database: EMDB / ID: EMD-2451
TitleCryo-EM structure of the CSFV IRES in complex with eIF3, small ribosomal 40S subunit and DHX29
Map dataReconstruction of a mutant Classical Swine Fever Virus IRES bound to eukaryotic initiation factor 3, the Rabbit 40S subunit and DHX29.
Sample
  • Sample: Reconstruction of a mutant Classical Swine Fever Virus IRES bound to eukaryotic initiation factor 3, the Rabbit 40S subunit and DHX29.
  • Complex: eukaryotic small ribosmal subunit
  • RNA: Internal Ribosomal Entry Site
  • Protein or peptide: DHX29
  • Protein or peptide: eukaryotic initiation factor 3
KeywordsInternal Ribosomal Entry Site / 5'-end independent initiation / HCV-like IRES / eIF3/HCV-like IRES interaction
Function / homology
Function and homology information


positive regulation of mRNA binding / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / translation reinitiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / cytoplasmic translational initiation ...positive regulation of mRNA binding / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / translation reinitiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / cytoplasmic translational initiation / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / metal-dependent deubiquitinase activity / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / negative regulation of translational initiation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / translation initiation factor binding / translation initiation factor activity / positive regulation of translation / translational initiation / PML body / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / fibrillar center / metallopeptidase activity / ribosome binding / ubiquitinyl hydrolase 1 / microtubule / cysteine-type deubiquitinase activity / postsynaptic density / cadherin binding / mRNA binding / synapse / chromatin / nucleolus / structural molecule activity / proteolysis / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit H / eIF3h, C-terminal / C-terminal region of eIF3h / Eukaryotic translation initiation factor 3 subunit F / Translation initiation factor 3 complex subunit L / RNA polymerase I-associated factor PAF67 / Eukaryotic translation initiation factor 3 subunit M / eIF3 subunit M, C-terminal helix domain / eIF3 subunit 6 N terminal domain / eIF3 subunit M, C-terminal helix ...Eukaryotic translation initiation factor 3 subunit H / eIF3h, C-terminal / C-terminal region of eIF3h / Eukaryotic translation initiation factor 3 subunit F / Translation initiation factor 3 complex subunit L / RNA polymerase I-associated factor PAF67 / Eukaryotic translation initiation factor 3 subunit M / eIF3 subunit M, C-terminal helix domain / eIF3 subunit 6 N terminal domain / eIF3 subunit M, C-terminal helix / Eukaryotic translation initiation factor 3 subunit E, C-terminal / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit E, N-terminal / eIF3 subunit 6 N terminal domain / Eukaryotic translation initiation factor 3 subunit K / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / eIF3a, PCI domain, TPR-like region / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / Eukaryotic translation initiation factor 3 subunit A / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / : / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit H / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit M / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit K / Eukaryotic translation initiation factor 3 subunit L
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Classical swine fever virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.3 Å
AuthorsHashem Y / des-Georges A / Dhote V / Langlois R / Liao HY / Grassucci RA / Pestova TV / Hellen CUT / Frank J
CitationJournal: Nature / Year: 2013
Title: Hepatitis-C-virus-like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit.
Authors: Yaser Hashem / Amedee des Georges / Vidya Dhote / Robert Langlois / Hstau Y Liao / Robert A Grassucci / Tatyana V Pestova / Christopher U T Hellen / Joachim Frank /
Abstract: Hepatitis C virus (HCV) and classical swine fever virus (CSFV) messenger RNAs contain related (HCV-like) internal ribosome entry sites (IRESs) that promote 5'-end independent initiation of ...Hepatitis C virus (HCV) and classical swine fever virus (CSFV) messenger RNAs contain related (HCV-like) internal ribosome entry sites (IRESs) that promote 5'-end independent initiation of translation, requiring only a subset of the eukaryotic initiation factors (eIFs) needed for canonical initiation on cellular mRNAs. Initiation on HCV-like IRESs relies on their specific interaction with the 40S subunit, which places the initiation codon into the P site, where it directly base-pairs with eIF2-bound initiator methionyl transfer RNA to form a 48S initiation complex. However, all HCV-like IRESs also specifically interact with eIF3 (refs 2, 5-7, 9-12), but the role of this interaction in IRES-mediated initiation has remained unknown. During canonical initiation, eIF3 binds to the 40S subunit as a component of the 43S pre-initiation complex, and comparison of the ribosomal positions of eIF3 and the HCV IRES revealed that they overlap, so that their rearrangement would be required for formation of ribosomal complexes containing both components. Here we present a cryo-electron microscopy reconstruction of a 40S ribosomal complex containing eIF3 and the CSFV IRES. Remarkably, although the position and interactions of the CSFV IRES with the 40S subunit in this complex are similar to those of the HCV IRES in the 40S-IRES binary complex, eIF3 is completely displaced from its ribosomal position in the 43S complex, and instead interacts through its ribosome-binding surface exclusively with the apical region of domain III of the IRES. Our results suggest a role for the specific interaction of HCV-like IRESs with eIF3 in preventing ribosomal association of eIF3, which could serve two purposes: relieving the competition between the IRES and eIF3 for a common binding site on the 40S subunit, and reducing formation of 43S complexes, thereby favouring translation of viral mRNAs.
History
DepositionSep 7, 2013-
Header (metadata) releaseSep 18, 2013-
Map releaseNov 13, 2013-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0385
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0385
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j8b
  • Surface level: 0.0385
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j8b
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2451-40S...

Downloads & links

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Map

FileDownload / File: emd_2451.map.gz / Format: CCP4 / Size: 39.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of a mutant Classical Swine Fever Virus IRES bound to eukaryotic initiation factor 3, the Rabbit 40S subunit and DHX29.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.25 Å/pix.
x 220 pix.
= 493.9 Å		2.25 Å/pix.
x 220 pix.
= 493.9 Å		2.25 Å/pix.
x 220 pix.
= 493.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0385 / Movie #1: 0.0385
Minimum - Maximum-0.04869587 - 0.14228088
Average (Standard dev.)0.00008203 (±0.01052825)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 493.89996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.2452.2452.245
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z493.900493.900493.900
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0490.1420.000

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Supplemental data

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Sample components

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Entire : Reconstruction of a mutant Classical Swine Fever Virus IRES bound...

EntireName: Reconstruction of a mutant Classical Swine Fever Virus IRES bound to eukaryotic initiation factor 3, the Rabbit 40S subunit and DHX29.
Components
  • Sample: Reconstruction of a mutant Classical Swine Fever Virus IRES bound to eukaryotic initiation factor 3, the Rabbit 40S subunit and DHX29.
  • Complex: eukaryotic small ribosmal subunit
  • RNA: Internal Ribosomal Entry Site
  • Protein or peptide: DHX29
  • Protein or peptide: eukaryotic initiation factor 3

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Supramolecule #1000: Reconstruction of a mutant Classical Swine Fever Virus IRES bound...

SupramoleculeName: Reconstruction of a mutant Classical Swine Fever Virus IRES bound to eukaryotic initiation factor 3, the Rabbit 40S subunit and DHX29.
type: sample / ID: 1000
Oligomeric state: one 40S, one CSFV IRES, one eIF3 and one DHX29
Number unique components: 4
Molecular weightTheoretical: 2.6 MDa

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Supramolecule #1: eukaryotic small ribosmal subunit

SupramoleculeName: eukaryotic small ribosmal subunit / type: complex / ID: 1 / Name.synonym: 40S subunit / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: SSU 40S, SSU RNA 18S
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: blood / Cell: reticulocytes
Molecular weightTheoretical: 1.5 MDa

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Macromolecule #1: Internal Ribosomal Entry Site

MacromoleculeName: Internal Ribosomal Entry Site / type: rna / ID: 1 / Name.synonym: IRES / Classification: OTHER / Structure: DOUBLE HELIX / Synthetic?: Yes
Source (natural)Organism: Classical swine fever virus / synonym: CSFV
Molecular weightTheoretical: 100 KDa
SequenceString: GACUAGCCGU AGUGGCGAGC UCCCUGGGUG GUCUAAGUCC UGAGUACAGG ACAGUCGUCA GUAGUUCGAC GUGAGCACUA GCCCACCUCG AGAUGCUACG UGGACGAGGG CAUGCCCAAG ACACACCUUA ACCCUGGCGG GGGUCGCUAG GGUGAAAUCA CAUUAUGUGA ...String:
GACUAGCCGU AGUGGCGAGC UCCCUGGGUG GUCUAAGUCC UGAGUACAGG ACAGUCGUCA GUAGUUCGAC GUGAGCACUA GCCCACCUCG AGAUGCUACG UGGACGAGGG CAUGCCCAAG ACACACCUUA ACCCUGGCGG GGGUCGCUAG GGUGAAAUCA CAUUAUGUGA UGGGGGUACG ACCUGAUAGG GUGCUGCAGA GGCCCACUAG CAGGCUAGUA UAAAAAUCUC UGC

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Macromolecule #2: DHX29

MacromoleculeName: DHX29 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 150 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #3: eukaryotic initiation factor 3

MacromoleculeName: eukaryotic initiation factor 3 / type: protein_or_peptide / ID: 3 / Name.synonym: eIF3 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulocytes
Molecular weightTheoretical: 850 KDa

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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

Concentration0.105 mg/mL
BufferpH: 7.5
Details: 20 mM Tris , 75 mM KCl, 5 mM Mg, 2 mM DTT and 0.25 mM spermidine
GridDetails: 300 mesh copper/molybdenum holey carbon-coated Quantifoil 2/4 grid (Quantifoil Micro Tools GmbH) containing an additional continuous thin layer of carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK II
Method: 30 seconds waiting after sample deposition on the grid, blotting for seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 110 K
DateFeb 1, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 12000 / Average electron dose: 12 e/Å2 / Bits/pixel: 32
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 51570 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: -4.0 µm / Nominal defocus min: -1.0 µm
Sample stageSpecimen holder: Gatan CT3500 side-entry cryo-holder / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsThe particles constituting this reconstruction were sorted using RELION.
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.3 Å / Resolution method: OTHER / Software - Name: Spider, Relion / Number images used: 26000

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