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Entry
Database: EMDB / ID: EMD-2813
TitleCryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus IRES reveal the IRES in the translocated state
Map dataReconstruction of mammalian termination complex with CrPV IRES-RNA, eRF1 and eRF3
Sample
  • Sample: Ribosomal 80S termination complex with CrPV IRES-RNA, eRF1 and eRF3
  • Complex: 80S ribosome
  • Protein or peptide: eukaryoric release factor 1
  • Protein or peptide: eukaryotic release factor 3
  • RNA: Cricket paralysis virus IRES RNA
KeywordsCrPV IRES / ribosome / Termination / release factors
Function / homology
Function and homology information


translation termination factor activity / translation release factor complex / cytoplasmic translational termination / regulation of translational termination / translation release factor activity, codon specific / protein methylation / translation release factor activity / sequence-specific mRNA binding / ribosomal subunit / peptidyl-tRNA hydrolase activity ...translation termination factor activity / translation release factor complex / cytoplasmic translational termination / regulation of translational termination / translation release factor activity, codon specific / protein methylation / translation release factor activity / sequence-specific mRNA binding / ribosomal subunit / peptidyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / laminin receptor activity / Protein hydroxylation / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / 90S preribosome / phagocytic cup / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translational termination / ribosomal small subunit export from nucleus / laminin binding / rough endoplasmic reticulum / translation regulator activity / gastrulation / MDM2/MDM4 family protein binding / cytosolic ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA / small-subunit processome / G1/S transition of mitotic cell cycle / Regulation of expression of SLITs and ROBOs / spindle / rRNA processing / rhythmic process / positive regulation of canonical Wnt signaling pathway / regulation of translation / ribosome binding / virus receptor activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / perikaryon / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic translation / cell differentiation / mitochondrial inner membrane / postsynaptic density / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cell division / DNA repair / GTPase activity / mRNA binding / apoptotic process / dendrite / synapse / centrosome / GTP binding / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / DNA binding / RNA binding / zinc ion binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Ataxin-2, C-terminal / Ataxin-2 C-terminal region / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 ...Ataxin-2, C-terminal / Ataxin-2 C-terminal region / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 / eRF1 domain 3 / eRF1_1 / : / GTP-eEF1A C-terminal domain-like / : / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Ubiquitin-like protein FUBI / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / : / Ribosomal protein S26e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S5, eukaryotic/archaeal / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / S27a-like superfamily / Translation elongation factor EFTu-like, domain 2 / 40S Ribosomal protein S10 / : / Ribosomal protein S7e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S17e, conserved site / Ribosomal protein S30 / Ribosomal protein S17e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Elongation factor Tu domain 2 / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S6, eukaryotic / Ribosomal protein S19A/S15e / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / : / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature.
Similarity search - Domain/homology
Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein uS5 ...Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS11 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS17 / 40S ribosomal protein S24 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS14 / Eukaryotic peptide chain release factor GTP-binding subunit ERF3A / Eukaryotic peptide chain release factor subunit 1 / Eukaryotic peptide chain release factor GTP-binding subunit ERF3B
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Homo sapiens (human) / Cricket paralysis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 8.9 Å
AuthorsMuhs M / Hilal T / Mielke T / Skabkin MA / Sanbonmatsu KY / Pestova TV / Spahn CMT
CitationJournal: Mol Cell / Year: 2015
Title: Cryo-EM of ribosomal 80S complexes with termination factors reveals the translocated cricket paralysis virus IRES.
Authors: Margarita Muhs / Tarek Hilal / Thorsten Mielke / Maxim A Skabkin / Karissa Y Sanbonmatsu / Tatyana V Pestova / Christian M T Spahn /
Abstract: The cricket paralysis virus (CrPV) uses an internal ribosomal entry site (IRES) to hijack the ribosome. In a remarkable RNA-based mechanism involving neither initiation factor nor initiator tRNA, the ...The cricket paralysis virus (CrPV) uses an internal ribosomal entry site (IRES) to hijack the ribosome. In a remarkable RNA-based mechanism involving neither initiation factor nor initiator tRNA, the CrPV IRES jumpstarts translation in the elongation phase from the ribosomal A site. Here, we present cryoelectron microscopy (cryo-EM) maps of 80S⋅CrPV-STOP ⋅ eRF1 ⋅ eRF3 ⋅ GMPPNP and 80S⋅CrPV-STOP ⋅ eRF1 complexes, revealing a previously unseen binding state of the IRES and directly rationalizing that an eEF2-dependent translocation of the IRES is required to allow the first A-site occupation. During this unusual translocation event, the IRES undergoes a pronounced conformational change to a more stretched conformation. At the same time, our structural analysis provides information about the binding modes of eRF1 ⋅ eRF3 ⋅ GMPPNP and eRF1 in a minimal system. It shows that neither eRF3 nor ABCE1 are required for the active conformation of eRF1 at the intersection between eukaryotic termination and recycling.
History
DepositionNov 6, 2014-
Header (metadata) releaseDec 24, 2014-
Map releaseFeb 4, 2015-
UpdateMar 11, 2015-
Current statusMar 11, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
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  • Surface view colored by height
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4d61, PDB-4d67
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4d61
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4d67
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

2813.png

Downloads & links

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Map

FileDownload / File: emd_2813.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of mammalian termination complex with CrPV IRES-RNA, eRF1 and eRF3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.56 Å/pix.
x 300 pix.
= 468. Å		1.56 Å/pix.
x 300 pix.
= 468. Å		1.56 Å/pix.
x 300 pix.
= 468. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.56 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-4.36269093 - 12.16475964
Average (Standard dev.)0.1640757 (±0.95369095)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-149
Dimensions300300300
Spacing300300300
CellA=B=C: 467.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.561.561.56
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z468.000468.000468.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-32-96
NX/NY/NZ8165193
MAP C/R/S123
start NC/NR/NS-150-150-149
NC/NR/NS300300300
D min/max/mean-4.36312.1650.164

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Supplemental data

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Sample components

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Entire : Ribosomal 80S termination complex with CrPV IRES-RNA, eRF1 and eRF3

EntireName: Ribosomal 80S termination complex with CrPV IRES-RNA, eRF1 and eRF3
Components
  • Sample: Ribosomal 80S termination complex with CrPV IRES-RNA, eRF1 and eRF3
  • Complex: 80S ribosome
  • Protein or peptide: eukaryoric release factor 1
  • Protein or peptide: eukaryotic release factor 3
  • RNA: Cricket paralysis virus IRES RNA

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Supramolecule #1000: Ribosomal 80S termination complex with CrPV IRES-RNA, eRF1 and eRF3

SupramoleculeName: Ribosomal 80S termination complex with CrPV IRES-RNA, eRF1 and eRF3
type: sample / ID: 1000
Oligomeric state: CrPV IRES, eRF1 and eRF3 bound to one 80S ribosome
Number unique components: 4
Molecular weightTheoretical: 4.5 MDa

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Supramolecule #1: 80S ribosome

SupramoleculeName: 80S ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit
Molecular weightTheoretical: 4.5 MDa

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Macromolecule #1: eukaryoric release factor 1

MacromoleculeName: eukaryoric release factor 1 / type: protein_or_peptide / ID: 1 / Name.synonym: eRF1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 50 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceUniProtKB: Eukaryotic peptide chain release factor subunit 1

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Macromolecule #2: eukaryotic release factor 3

MacromoleculeName: eukaryotic release factor 3 / type: protein_or_peptide / ID: 2 / Name.synonym: eRF3 / Details: N-terminal 138 aa truncated / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 68.8 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceUniProtKB: Eukaryotic peptide chain release factor GTP-binding subunit ERF3B

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Macromolecule #3: Cricket paralysis virus IRES RNA

MacromoleculeName: Cricket paralysis virus IRES RNA / type: rna / ID: 3 / Name.synonym: CrPV IRES RNA / Classification: OTHER / Structure: OTHER / Synthetic?: No
Source (natural)Organism: Cricket paralysis virus
SequenceString: AAAAAUGUGA UCUUGCUUGU AAAUACAAUU UUGAGAGGUU AAUAAAUUAC AAGUAGUGCU AUUUUUGUAU UUAGGUUAGC UAUUUAGCUU UACGUUCCAG GAUGCCUAGU GGCAGCCCCA CAAUAUCCAG GAAGCCCUCU CUGCGGUUUU UCAGAUUAGG UAGUCGAAAA ...String:
AAAAAUGUGA UCUUGCUUGU AAAUACAAUU UUGAGAGGUU AAUAAAUUAC AAGUAGUGCU AUUUUUGUAU UUAGGUUAGC UAUUUAGCUU UACGUUCCAG GAUGCCUAGU GGCAGCCCCA CAAUAUCCAG GAAGCCCUCU CUGCGGUUUU UCAGAUUAGG UAGUCGAAAA ACCUAAGAAA UUUACCUUAA GGCUUCCUCG A

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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

Concentration1.38 mg/mL
BufferpH: 7.5
Details: 20 mM Tris pH 7.5, 100 mM KCl, 1 mM DTT, 8.5 mM MgCl2, 0.133 mM GTP, 2.33 mM GMPPNP
GridDetails: Quantifoil grids with additional continuous carbon support
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Instrument: FEI VITROBOT MARK II / Method: blot for 2/4 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 77 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification
Detailsminimal dose system
DateNov 5, 2012
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 26959 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 194805 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 115000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsThe particles were selected using SIGNATURE and processed by using SPIDER and SPARX
CTF correctionDetails: Defocus group
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.9 Å / Resolution method: OTHER / Software - Name: SPIDER, SPARX
Details: The particles were selected using SIGNATURE and processed by using SPIDER and SPARX.
Number images used: 64902

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Atomic model buiding 1

Initial modelPDB ID:

4cxc
PDB Unreleased entry


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G / Chain - #7 - Chain ID: H / Chain - #8 - Chain ID: I / Chain - #9 - Chain ID: J / Chain - #10 - Chain ID: K / Chain - #11 - Chain ID: L / Chain - #12 - Chain ID: M / Chain - #13 - Chain ID: N / Chain - #14 - Chain ID: O / Chain - #15 - Chain ID: P / Chain - #16 - Chain ID: Q / Chain - #17 - Chain ID: R / Chain - #18 - Chain ID: S / Chain - #19 - Chain ID: T / Chain - #20 - Chain ID: U / Chain - #21 - Chain ID: V / Chain - #22 - Chain ID: W / Chain - #23 - Chain ID: X / Chain - #24 - Chain ID: Y / Chain - #25 - Chain ID: Z / Chain - #26 - Chain ID: a / Chain - #27 - Chain ID: b / Chain - #28 - Chain ID: c / Chain - #29 - Chain ID: d / Chain - #30 - Chain ID: e / Chain - #31 - Chain ID: f / Chain - #32 - Chain ID: g / Chain - #33 - Chain ID: 1
SoftwareName: CHIMERA
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4d61:
Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus IRES reveal the IRES in the translocated state

PDB-4d67:
Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus IRES reveal the IRES in the translocated state

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Atomic model buiding 2

Initial modelPDB ID:

4cxd
PDB Unreleased entry


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G / Chain - #7 - Chain ID: H / Chain - #8 - Chain ID: I / Chain - #9 - Chain ID: J / Chain - #10 - Chain ID: L / Chain - #11 - Chain ID: M / Chain - #12 - Chain ID: N / Chain - #13 - Chain ID: O / Chain - #14 - Chain ID: P / Chain - #15 - Chain ID: Q / Chain - #16 - Chain ID: R / Chain - #17 - Chain ID: S / Chain - #18 - Chain ID: T / Chain - #19 - Chain ID: U / Chain - #20 - Chain ID: V / Chain - #21 - Chain ID: W / Chain - #22 - Chain ID: X / Chain - #23 - Chain ID: Y / Chain - #24 - Chain ID: Z / Chain - #25 - Chain ID: a / Chain - #26 - Chain ID: b / Chain - #27 - Chain ID: c / Chain - #28 - Chain ID: d / Chain - #29 - Chain ID: e / Chain - #30 - Chain ID: f / Chain - #31 - Chain ID: g / Chain - #32 - Chain ID: h / Chain - #33 - Chain ID: i / Chain - #34 - Chain ID: j / Chain - #35 - Chain ID: k / Chain - #36 - Chain ID: l / Chain - #37 - Chain ID: m / Chain - #38 - Chain ID: n / Chain - #39 - Chain ID: o / Chain - #40 - Chain ID: p / Chain - #41 - Chain ID: t / Chain - #42 - Chain ID: u
SoftwareName: CHIMERA
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4d61:
Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus IRES reveal the IRES in the translocated state

PDB-4d67:
Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus IRES reveal the IRES in the translocated state

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