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- EMDB-3221: Mammalian 80S HCV-IRES complex, Classical -

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Entry
Database: EMDB / ID: EMD-3221
TitleMammalian 80S HCV-IRES complex, Classical
Map dataReconstruction of ribosome complex
Sample
  • Sample: Mammalian 80S-HCV-IRES complex, classical
  • Complex: 80S ribosome
  • RNA: HCV-IRES
Keywordsribosome / translation initiation / Hepatitis C Virus internal ribosome entry site
Function / homology
Function and homology information


negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / positive regulation of ubiquitin-protein transferase activity / positive regulation of gastrulation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex ...negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / positive regulation of ubiquitin-protein transferase activity / positive regulation of gastrulation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / nucleolus organization / positive regulation of DNA-templated transcription initiation / TNFR1-mediated ceramide production / negative regulation of RNA splicing / supercoiled DNA binding / neural crest cell differentiation / NF-kappaB complex / negative regulation of DNA repair / oxidized purine DNA binding / cytoplasmic translational initiation / cysteine-type endopeptidase activator activity involved in apoptotic process / regulation of establishment of cell polarity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of bicellular tight junction assembly / rRNA modification in the nucleus and cytosol / ubiquitin-like protein conjugating enzyme binding / negative regulation of phagocytosis / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / protein kinase A binding / ion channel inhibitor activity / Ribosomal scanning and start codon recognition / laminin receptor activity / pigmentation / Translation initiation complex formation / positive regulation of mitochondrial depolarization / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / monocyte chemotaxis / BH3 domain binding / negative regulation of translational frameshifting / TOR signaling / Protein hydroxylation / SARS-CoV-1 modulates host translation machinery / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / mTORC1-mediated signalling / positive regulation of GTPase activity / iron-sulfur cluster binding / Peptide chain elongation / regulation of cell division / Selenocysteine synthesis / cellular response to ethanol / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / SRP-dependent cotranslational protein targeting to membrane / protein serine/threonine kinase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of protein binding / Viral mRNA Translation / ubiquitin ligase inhibitor activity / negative regulation of respiratory burst involved in inflammatory response / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of signal transduction by p53 class mediator / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of ubiquitin-dependent protein catabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / positive regulation of microtubule polymerization / regulation of translational fidelity / phagocytic cup / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / positive regulation of intrinsic apoptotic signaling pathway / spindle assembly / Protein methylation / 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) / Nuclear events stimulated by ALK signaling in cancer / translation regulator activity / rough endoplasmic reticulum / positive regulation of cell cycle / ribosomal small subunit export from nucleus / laminin binding / translation initiation factor binding / gastrulation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Maturation of protein E / DNA-(apurinic or apyrimidinic site) endonuclease activity / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / signaling adaptor activity / MDM2/MDM4 family protein binding / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis
Similarity search - Function
40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / : / Ribosomal protein S26e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. ...40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / : / 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 / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / S27a-like superfamily / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S10, eukaryotic/archaeal / : / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S7e signature. / Ribosomal protein S27a / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S27e signature. / Ribosomal protein S6, eukaryotic / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / 40S ribosomal protein S1/3, eukaryotes / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / : / 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 S28e conserved site / Ribosomal protein S28e signature. / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S6e signature. / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S8e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal
Similarity search - Domain/homology
Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein eS4, Y isoform 1 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 ...Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein eS4, Y isoform 1 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS28 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Hepatitis C virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsYamamoto H / Collier M / Loerke J / Ismer J / Schmidt A / Hilal T / Sprink T / Yamamoto K / Mielke T / Burger J ...Yamamoto H / Collier M / Loerke J / Ismer J / Schmidt A / Hilal T / Sprink T / Yamamoto K / Mielke T / Burger J / Shaikh TR / Dabrowski M / Hildebrand PW / Scheerer P / Spahn CMT
CitationJournal: EMBO J / Year: 2015
Title: Molecular architecture of the ribosome-bound Hepatitis C Virus internal ribosomal entry site RNA.
Authors: Hiroshi Yamamoto / Marianne Collier / Justus Loerke / Jochen Ismer / Andrea Schmidt / Tarek Hilal / Thiemo Sprink / Kaori Yamamoto / Thorsten Mielke / Jörg Bürger / Tanvir R Shaikh / ...Authors: Hiroshi Yamamoto / Marianne Collier / Justus Loerke / Jochen Ismer / Andrea Schmidt / Tarek Hilal / Thiemo Sprink / Kaori Yamamoto / Thorsten Mielke / Jörg Bürger / Tanvir R Shaikh / Marylena Dabrowski / Peter W Hildebrand / Patrick Scheerer / Christian M T Spahn /
Abstract: Internal ribosomal entry sites (IRESs) are structured cis-acting RNAs that drive an alternative, cap-independent translation initiation pathway. They are used by many viruses to hijack the ...Internal ribosomal entry sites (IRESs) are structured cis-acting RNAs that drive an alternative, cap-independent translation initiation pathway. They are used by many viruses to hijack the translational machinery of the host cell. IRESs facilitate translation initiation by recruiting and actively manipulating the eukaryotic ribosome using only a subset of canonical initiation factor and IRES transacting factors. Here we present cryo-EM reconstructions of the ribosome 80S- and 40S-bound Hepatitis C Virus (HCV) IRES. The presence of four subpopulations for the 80S•HCV IRES complex reveals dynamic conformational modes of the complex. At a global resolution of 3.9 Å for the most stable complex, a derived atomic model reveals a complex fold of the IRES RNA and molecular details of its interaction with the ribosome. The comparison of obtained structures explains how a modular architecture facilitates mRNA loading and tRNA binding to the P-site. This information provides the structural foundation for understanding the mechanism of HCV IRES RNA-driven translation initiation.
History
DepositionOct 27, 2015-
Header (metadata) releaseNov 25, 2015-
Map releaseDec 16, 2015-
UpdateJan 13, 2016-
Current statusJan 13, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
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  • Surface view colored by height
  • Surface level: 2.5
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  • Surface view with fitted model
  • Atomic models: PDB-5flx
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5flx
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Movie viewer
Structure viewerEM map:
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Supplemental images

EMD-1-3221.png

Downloads & links

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Map

FileDownload / File: emd_3221.map.gz / Format: CCP4 / Size: 204.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of ribosome complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.07 Å/pix.
x 380 pix.
= 406.6 Å		1.07 Å/pix.
x 380 pix.
= 406.6 Å		1.07 Å/pix.
x 380 pix.
= 406.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 3.0 / Movie #1: 2.5
Minimum - Maximum-10.56054211 - 17.786176680000001
Average (Standard dev.)-0.00795648 (±0.9967249)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-190-190-189
Dimensions380380380
Spacing380380380
CellA=B=C: 406.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z406.600406.600406.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-189
NX/NY/NZ380380380
MAP C/R/S213
start NC/NR/NS-190-190-189
NC/NR/NS380380380
D min/max/mean-10.56117.786-0.008

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Supplemental data

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Sample components

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Entire : Mammalian 80S-HCV-IRES complex, classical

EntireName: Mammalian 80S-HCV-IRES complex, classical
Components
  • Sample: Mammalian 80S-HCV-IRES complex, classical
  • Complex: 80S ribosome
  • RNA: HCV-IRES

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Supramolecule #1000: Mammalian 80S-HCV-IRES complex, classical

SupramoleculeName: Mammalian 80S-HCV-IRES complex, classical / type: sample / ID: 1000 / Number unique components: 2
Molecular weightTheoretical: 4.6 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 / Tissue: reticulocyte lysate
Molecular weightTheoretical: 4.5 MDa

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Macromolecule #1: HCV-IRES

MacromoleculeName: HCV-IRES / type: rna / ID: 1 / Classification: OTHER / Structure: DOUBLE HELIX / Synthetic?: Yes
Source (natural)Organism: Hepatitis C virus / synonym: HCV
Molecular weightTheoretical: 162 KDa
SequenceString: GCCAGCCCCC UGAUGGGGGC GACACUCCAC CAUGAAUCAC UCCCCUGUGA GGAACUACUG UCUUCACGCA GAAAGCGUCU AGCCAUGGCG UUAGUAUGAG UGUCGUGCAG CCUCCAGGAC CCCCCCUCCC GGGAGAGCCA UAGUGGUCUG CGGAACCGGU GAGUACACCG ...String:
GCCAGCCCCC UGAUGGGGGC GACACUCCAC CAUGAAUCAC UCCCCUGUGA GGAACUACUG UCUUCACGCA GAAAGCGUCU AGCCAUGGCG UUAGUAUGAG UGUCGUGCAG CCUCCAGGAC CCCCCCUCCC GGGAGAGCCA UAGUGGUCUG CGGAACCGGU GAGUACACCG GAAUUGCCAG GACGACCGGG UCCUUUCUUG GAUAAACCCG CUCAAUGCCU GGAGAUUUGG GCGUGCCCCC GCAAGACUGC UAGCCGAGUA GUGUUGGGUC GCGAAAGGCC UUGUGGUACU GCCUGAUAGG GUGCUUGCGA GUGCCCCGGG AGGUCUCGUA GACCGUGCAC CAUGAGCACG AAUCCUAAAC CUCAAAGAAA AACCAAACGU AACACCAACC GUCGCCCACA GGACGUCAAG UUCCCGGGUG GCGGUCUAGA CGCCGAGAUC AGAAAUCCCU CUCUCGGAUC GCAUUUGGAC UUCUGCCUUC GGGCACCACG GUCGGAUCCG AAUU

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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

Concentration0.15 mg/mL
BufferpH: 7.6
Details: 20mM Tris-HCl, 7.5mM MgCl2, 100mM KCl, 0.2mM spermidine, 2mM DTT
GridDetails: Quantifoil R3-3 Cu 300 mesh with 2 nm carbon support film
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 93 K / Instrument: FEI VITROBOT MARK I / Method: blot for 2-4 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateOct 16, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 7707 / Average electron dose: 20 e/Å2 / Details: Automated data collection on using EPU
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 130293 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: CTFFIND3
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: OTHER / Software - Name: spider, sparx
Details: To avoid overfitting, the data was refined in a resolution-limited scheme using SPIDER. A final local refinement and the final reconstruction were calculated in Sparx.
Number images used: 171820

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Atomic model buiding 1

Initial modelPDB ID:

5aj0

SoftwareName: chimera
RefinementSpace: REAL
Output model

PDB-5flx:
Mammalian 40S HCV-IRES complex

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