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- EMDB-21530: Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-I... -

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Basic information

Entry
Database: EMDB / ID: EMD-21530
TitleStructure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2)
Map data
SampleStructure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2)
  • (nucleic-acidNucleic acid) x 2
  • uS2
  • eS1
  • uS5
  • eS4
  • eS6
  • eS7
  • eS8
  • uS4
  • uS17
  • uS15
  • uS11
  • eS21
  • uS8
  • uS12
  • eS24
  • eS26
  • eS27
  • eS30
  • uS3
  • uS7
  • eS10
  • eS12
  • uS19
  • uS9
  • eS17
  • uS13
  • eS19
  • uS10
  • eS25
  • eS28
  • eS29
  • eS31
  • RACK1Receptor for activated C kinase 1
  • (Eukaryotic translation initiation factor 3 subunit ...) x 9
  • (ligand) x 2
Function / homology
Function and homology information


cap-dependent translational initiation / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / mRNA cap binding / IRES-dependent viral translational initiation / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex ...cap-dependent translational initiation / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / mRNA cap binding / IRES-dependent viral translational initiation / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / laminin receptor activity / response to TNF agonist / positive regulation of base-excision repair / negative regulation of DNA repair / positive regulation of DNA N-glycosylase activity / oxidized pyrimidine DNA binding / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / regulation of translational initiation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / mammalian oogenesis stage / NF-kappaB complex / positive regulation of endodeoxyribonuclease activity / oxidized purine DNA binding / protein kinase A binding / activation-induced cell death of T cells / supercoiled DNA binding / ubiquitin-like protein conjugating enzyme binding / positive regulation of T cell receptor signaling pathway / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of activated T cell proliferation / erythrocyte development / TOR signaling / T cell proliferation involved in immune response / spindle assembly / positive regulation of JUN kinase activity / isopeptidase activity / ribosomal small subunit biogenesis / translation initiation factor binding / gastrulation / positive regulation of microtubule polymerization / polysome / laminin binding / Hsp70 protein binding / translation initiation factor activity / polysomal ribosome / negative regulation of protein ubiquitination / endodeoxyribonuclease activity / positive regulation of interleukin-2 production / fibrillar center / rough endoplasmic reticulum / mitotic spindle / ribosomal small subunit assembly / cytoplasmic ribonucleoprotein granule / chromosome segregation / ruffle membrane / Hsp90 protein binding / small ribosomal subunit rRNA binding / DNA damage response, detection of DNA damage / placenta development / rRNA processing / PML body / metallopeptidase activity / positive regulation of NIK/NF-kappaB signaling / cellular response to hydrogen peroxide / cytoplasmic translation / G1/S transition of mitotic cell cycle / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cell body / ribosome binding / thiol-dependent deubiquitinase / cellular response to tumor necrosis factor / cytosolic small ribosomal subunit / glucose homeostasis / small ribosomal subunit / mitochondrial inner membrane / T cell differentiation in thymus / microtubule binding / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / postsynaptic density / positive regulation of NF-kappaB transcription factor activity / mitochondrial matrix / protein deubiquitination / cell differentiation / translation / cell division / mRNA binding / transcription factor binding / positive regulation of apoptotic process / dendrite / apoptotic process / protein-containing complex binding / nucleolus / positive regulation of cell population proliferation / protein kinase binding / negative regulation of apoptotic process / Golgi apparatus
Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S5 / Ribosomal protein S15 / Ribosomal protein S27e / Ubiquitin-like domain / Ribosomal protein S8 / Proteasome component (PCI) domain / Ribosomal protein S9 / Ribosomal protein S4e / Ribosomal protein S7e ...Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S5 / Ribosomal protein S15 / Ribosomal protein S27e / Ubiquitin-like domain / Ribosomal protein S8 / Proteasome component (PCI) domain / Ribosomal protein S9 / Ribosomal protein S4e / Ribosomal protein S7e / Ribosomal protein S26e / Ribosomal protein S8e / Ribosomal protein S14 / Ribosomal protein S17e / Ribosomal protein S19e / Ribosomal protein S3, C-terminal / Ribosomal protein S6e / JAB1/MPN/MOV34 metalloenzyme domain / Ribosomal protein S12e / WD40 repeat / WD40-repeat-containing domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S6, eukaryotic / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal S24e conserved site / Ribosomal protein S4, conserved site / Eukaryotic translation initiation factor 3 subunit E / Ribosomal protein S28e / Armadillo-type fold / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / K homology domain-like, alpha/beta / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein L2, domain 2 / Ribosomal protein S5/S7 / Ribosomal protein S17/S11 / Ribosomal protein S3Ae / Ribosomal protein S10 / Ribosomal protein S13, conserved site / Eukaryotic translation initiation factor 3 subunit K / KOW / Ribosomal protein S12/S23 / Ribosomal protein S30 / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / K homology domain superfamily, prokaryotic type / S15/NS1, RNA-binding / Ribosomal protein S13-like, H2TH / Ribosomal protein S5/S7, eukaryotic/archaeal / Zinc-binding ribosomal protein / Tetratricopeptide-like helical domain superfamily / Nucleic acid-binding, OB-fold / Ribosomal protein S13/S15, N-terminal / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein S5, N-terminal / Ribosomal protein S4e, N-terminal / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein S2 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein S13 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S11 / Ribosomal protein S24e / Ribosomal protein S19/S15 / Ribosomal protein S27a / RNA-binding S4 domain / K Homology domain, type 2 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S5, C-terminal / Plectin/S10, N-terminal / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S10, conserved site / Ribosomal protein S4e, central region / Ribosomal protein S10 domain / Eukaryotic translation initiation factor 3 subunit M / 40S ribosomal protein S4, C-terminal domain / Ubiquitin-like domain superfamily / 50S ribosomal protein L30e-like / Ribosomal protein S4, KOW domain / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit H / 40S ribosomal protein S11, N-terminal / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit A / 40S ribosomal protein SA / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S2, eukaryotic / 30s ribosomal protein S13, C-terminal / Rpn11/EIF3F, C-terminal / 40S ribosomal protein SA, C-terminal domain / CSN8/PSMD8/EIF3K / Ribosomal protein S19, superfamily
40S ribosomal protein S18 / 40S ribosomal protein S15a / 40S ribosomal protein S28 / 40S ribosomal protein S8 / 40S ribosomal protein S4 / 40S ribosomal protein S6 / 40S ribosomal protein S19 / 40S ribosomal protein S3 / 40S ribosomal protein SA / S10_plectin domain-containing protein ...40S ribosomal protein S18 / 40S ribosomal protein S15a / 40S ribosomal protein S28 / 40S ribosomal protein S8 / 40S ribosomal protein S4 / 40S ribosomal protein S6 / 40S ribosomal protein S19 / 40S ribosomal protein S3 / 40S ribosomal protein SA / S10_plectin domain-containing protein / 40S ribosomal protein S11 / 40S ribosomal protein S17 / 40S ribosomal protein S26 / 40S ribosomal protein S27 / 40S ribosomal protein S15 / Uncharacterized protein / 40S ribosomal protein S29 / Eukaryotic translation initiation factor 3 subunit C / Ribosomal protein S5 / 40S ribosomal protein S23 / 40S ribosomal protein S25 / Eukaryotic translation initiation factor 3 subunit M / 40S ribosomal protein S9 / Eukaryotic translation initiation factor 3 subunit L / 40S ribosomal protein S12 / Uncharacterized protein / 40S ribosomal protein S20 / WD_REPEATS_REGION domain-containing protein / 40S ribosomal protein S27a / Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit A / 40S ribosomal protein S30 / 40S ribosomal protein S13 / 40S ribosomal protein S3a / Eukaryotic translation initiation factor 3 subunit H / Eukaryotic translation initiation factor 3 subunit E / 40S ribosomal protein S7 / 40S ribosomal protein S2 / 40S ribosomal protein S24 / Eukaryotic translation initiation factor 3 subunit K / Eukaryotic translation initiation factor 3 subunit D
Biological speciesOryctolagus cuniculus (rabbit) / Rabbit (rabbit) / Cricket paralysis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsNeupane R / Pisareva V / Rodriguez CF / Pisarev A / Fernandez IS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097014 United States
CitationJournal: Elife / Year: 2020
Title: A complex IRES at the 5'-UTR of a viral mRNA assembles a functional 48S complex via an uAUG intermediate.
Authors: Ritam Neupane / Vera P Pisareva / Carlos F Rodriguez / Andrey V Pisarev / Israel S Fernández /
Abstract: Taking control of the cellular apparatus for protein production is a requirement for virus progression. To ensure this control, diverse strategies of cellular mimicry and/or ribosome hijacking have ...Taking control of the cellular apparatus for protein production is a requirement for virus progression. To ensure this control, diverse strategies of cellular mimicry and/or ribosome hijacking have evolved. The initiation stage of translation is especially targeted as it involves multiple steps and the engagement of numerous initiation factors. The use of structured RNA sequences, called nternal ibosomal ntry ites (IRES), in viral RNAs is a widespread strategy for the exploitation of eukaryotic initiation. Using a combination of electron cryo-microscopy (cryo-EM) and reconstituted translation initiation assays with native components, we characterized how a novel IRES at the 5'-UTR of a viral RNA assembles a functional initiation complex via an uAUG intermediate. The IRES features a novel extended, multi-domain architecture, that circles the 40S head. The structures and accompanying functional data illustrate the importance of 5'-UTR regions in translation regulation and underline the relevance of the untapped diversity of viral IRESs.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionMar 8, 2020-
Header (metadata) releaseApr 22, 2020-
Map releaseApr 22, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6w2t
  • Surface level: 0.018
  • 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_21530.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424.2 Å
1.06 Å/pix.
x 400 pix.
= 424.2 Å
1.06 Å/pix.
x 400 pix.
= 424.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0605 Å
Density
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.10054721 - 0.1714331
Average (Standard dev.)0.00037778862 (±0.0043628775)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 424.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06051.06051.0605
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z424.200424.200424.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1010.1710.000

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Supplemental data

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Segmentation: #1

Fileemd_21530_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Additional map: Unsharpened map before post-processing for Class 2 (closed)

Fileemd_21530_additional.map
AnnotationUnsharpened map before post-processing for Class 2 (closed)
Projections & Slices
AxesZYX

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Half map: Half map 2 for Class 2 (closed)

Fileemd_21530_half_map_1.map
AnnotationHalf map 2 for Class 2 (closed)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map 1 for Class 2 (closed)

Fileemd_21530_half_map_2.map
AnnotationHalf map 1 for Class 2 (closed)
Projections & Slices
AxesZYX

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Sample components

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Entire Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-I...

EntireName: Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2)
Number of components: 47

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Component #1: protein, Structure of the Cricket Paralysis Virus 5-UTR IRES (CrP...

ProteinName: Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2)
Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #2: nucleic-acid, 18S rRNA

nucleic acidName: 18S rRNA18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: UACCUGGUUG AUCCUGCCAG UAGCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGCG AAUGGCUCAU UAAAUCAGUU AUGGUUCCUU UGGUCGCUCG ACUUGGAUAA CUGUGGUAAU UCUAGAGCUA AUACAUGCCG ...Sequence:
UACCUGGUUG AUCCUGCCAG UAGCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGCG AAUGGCUCAU UAAAUCAGUU AUGGUUCCUU UGGUCGCUCG ACUUGGAUAA CUGUGGUAAU UCUAGAGCUA AUACAUGCCG ACGGGCGCUG ACCCCCUUCG CGGGGGGGAU GCGUGCAUUU AUCAGUGGUG ACUCUAGAUA ACCUCGGGCC GAUCGCACGC CCGGCGGCGA CGACCCAUUC GAACGUCUGC CCUAUCAACU UUCGAUGGUA GUCGCCGUGC CUACCAUGGU GACCACGGGU GACGGGGAAU CAGGGUUCGA UUCCGGAGAG GGAGCCUGAG AAACGGCUAC CACAUCCAAG GAAGGCAGCA GGCGCGCAAA UUACCCACUC CCGACCCGGG GAGGUAGUGA CGAAAAAUAA CAAUACAGGA CUCUUUCGAG GCCCUGUAAU UGGAAUGAGU CCACUUUAAA UCCUUUAACG AGGAUCCAUU GGAGGGCAAG UCUGGUGCCA GCAGCCGCGG UAAUUCCAGC UCCAAUAGCG UAUAUUAAAG UUGCUGCAGU UAAAAAGCUC GUAGUUGGAU CUUGGGAGCG GCCGUCCCCU GCUCGGCGCC GGCCCGAAGC GUUUACUUUG AAAAAAUUAG AGUGUUCAAA GCAGGCCGCC UGGAUACCGC AGCUAGGAAU AAUGGAAUAG GACCGCGGUU CUAUUUUGUU GGUUUUCGGA ACUGAGGCCA UGAUUAAGAG GGACGGCCGG GGGCAUUCGU AUUGCGCCGC UAGAGGUGAA AUUCUUGGAC CGGCGCAAGA CGGACCAGAG CGAAAGCAUU UGCCAAGAAU GUUUUCAUUA AUCAAGAACG AAAGUCGGAG GUUCGAAGAC GAUCAGAUAC CGUCGUAGUU CCGACCAUAA ACGAUGCCGA CCGGCGAUGC GGCGGCGUUA UUCCCAUGAC CCGCCGGGCA GCUUCCGGGA AACCAAAGUC UUUGGGUUCC GGGGGGAGUA UGGUUGCAAA GCUGAAACUU AAAGGAAUUG ACGGAAGGGC ACCACCAGGA GUGGAGCCUG CGGCUUAAUU UGACUCAACA CGGGAAACCU CACCCGGCCC GGACACGGAC AGGAUUGACA GAUUGAUAGC UCUUUCUCGA UUCCGUGGGU GGUGGUGCAU GGCCGUUCUU AGUUGGUGGA GCGAUUUGUC UGGUUAAUUC CGAUAACGAA CGAGACUCUG GCAUGCUAAC UAGUUACGCG ACCCCGGUCG GCGUAACUUC UUAGAGGGAC AAGUGGCGUU CAGCCACCCG AGAUUGAGCA AUAACAGGUC UGUGAUGCCC UUAGAUGUCC GGGGCUGCAC GCGCGCUACA CUGACUGGCU CAGCGUGUGC CUACCCUACG CCGGCAGGCG CGGGUAACCC GUUGAACCCC AUUCGUGAUG GGGAUCGGGG AUUGCAAUUA UUCCCCAUGA ACGAGGAAUU CCCAGUAAGU GCGGGUCAUA AGCUUGCGUU GAUUAAGUCC CUGCCCUUUG UACACACCGC CCGUCGCUAC UACCGAUUGG AUGGUUUAGU GAGGCCCUCG GAUCGGCCCC GCCGGGGUGC CCUGGCGGAG CGCUGAGAAG ACGGUCGAAC UUGACUAUCU AGAGGAAGUA AAAGUCGUAA CAAGGUUUCC GUAGGUGAAC CUGCGGAAGG AUCAUUA
MassTheoretical: 547.733062 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #3: protein, uS2

ProteinName: uS2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.022055 kDa
SourceSpecies: Rabbit (rabbit)

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Component #4: protein, eS1

ProteinName: eS1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.002061 kDa
SourceSpecies: Rabbit (rabbit)

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Component #5: protein, uS5

ProteinName: uS5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.529238 kDa
SourceSpecies: Rabbit (rabbit)

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Component #6: protein, eS4

ProteinName: eS4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.59683 kDa
SourceSpecies: Rabbit (rabbit)

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Component #7: protein, eS6

ProteinName: eS6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.751906 kDa
SourceSpecies: Rabbit (rabbit)

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Component #8: protein, eS7

ProteinName: eS7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.168914 kDa
SourceSpecies: Rabbit (rabbit)

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Component #9: protein, eS8

ProteinName: eS8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.263387 kDa
SourceSpecies: Rabbit (rabbit)

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Component #10: protein, uS4

ProteinName: uS4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.641564 kDa
SourceSpecies: Rabbit (rabbit)

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Component #11: protein, uS17

ProteinName: uS17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.468826 kDa
SourceSpecies: Rabbit (rabbit)

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Component #12: protein, uS15

ProteinName: uS15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.259389 kDa
SourceSpecies: Rabbit (rabbit)

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Component #13: protein, uS11

ProteinName: uS11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.302772 kDa
SourceSpecies: Rabbit (rabbit)

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Component #14: protein, eS21

ProteinName: eS21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.098287 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #15: protein, uS8

ProteinName: uS8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.865555 kDa
SourceSpecies: Rabbit (rabbit)

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Component #16: protein, uS12

ProteinName: uS12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.784549 kDa
SourceSpecies: Rabbit (rabbit)

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Component #17: protein, eS24

ProteinName: eS24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.548398 kDa
SourceSpecies: Rabbit (rabbit)

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Component #18: protein, eS26

ProteinName: eS26 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.015506 kDa
SourceSpecies: Rabbit (rabbit)

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Component #19: protein, eS27

ProteinName: eS27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.480186 kDa
SourceSpecies: Rabbit (rabbit)

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Component #20: protein, eS30

ProteinName: eS30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.498884 kDa
SourceSpecies: Rabbit (rabbit)

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Component #21: protein, uS3

ProteinName: uS3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.146607 kDa
SourceSpecies: Rabbit (rabbit)

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Component #22: protein, uS7

ProteinName: uS7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.913453 kDa
SourceSpecies: Rabbit (rabbit)

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Component #23: protein, eS10

ProteinName: eS10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.156865 kDa
SourceSpecies: Rabbit (rabbit)

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Component #24: protein, eS12

ProteinName: eS12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.538987 kDa
SourceSpecies: Rabbit (rabbit)

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Component #25: protein, uS19

ProteinName: uS19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.049182 kDa
SourceSpecies: Rabbit (rabbit)

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Component #26: protein, uS9

ProteinName: uS9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.213465 kDa
SourceSpecies: Rabbit (rabbit)

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Component #27: protein, eS17

ProteinName: eS17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.552119 kDa
SourceSpecies: Rabbit (rabbit)

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Component #28: protein, uS13

ProteinName: uS13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.759777 kDa
SourceSpecies: Rabbit (rabbit)

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Component #29: protein, eS19

ProteinName: eS19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.235796 kDa
SourceSpecies: Rabbit (rabbit)

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Component #30: protein, uS10

ProteinName: uS10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.398763 kDa
SourceSpecies: Rabbit (rabbit)

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Component #31: protein, eS25

ProteinName: eS25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.776224 kDa
SourceSpecies: Rabbit (rabbit)

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Component #32: protein, eS28

ProteinName: eS28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.855052 kDa
SourceSpecies: Rabbit (rabbit)

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Component #33: protein, eS29

ProteinName: eS29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.690821 kDa
SourceSpecies: Rabbit (rabbit)

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Component #34: protein, eS31

ProteinName: eS31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.004041 kDa
SourceSpecies: Rabbit (rabbit)

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Component #35: protein, RACK1

ProteinName: RACK1Receptor for activated C kinase 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.115652 kDa
SourceSpecies: Rabbit (rabbit)

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Component #36: protein, Eukaryotic translation initiation factor 3 subunit E

ProteinName: Eukaryotic translation initiation factor 3 subunit E / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.199863 kDa
SourceSpecies: Rabbit (rabbit)

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Component #37: protein, Eukaryotic translation initiation factor 3 subunit F

ProteinName: Eukaryotic translation initiation factor 3 subunit F / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.84673 kDa
SourceSpecies: Rabbit (rabbit)

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Component #38: protein, Eukaryotic translation initiation factor 3 subunit K

ProteinName: Eukaryotic translation initiation factor 3 subunit K / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.129709 kDa
SourceSpecies: Rabbit (rabbit)

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Component #39: protein, Eukaryotic translation initiation factor 3 subunit L

ProteinName: Eukaryotic translation initiation factor 3 subunit L / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 71.001477 kDa
SourceSpecies: Rabbit (rabbit)

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Component #40: protein, Eukaryotic translation initiation factor 3 subunit M

ProteinName: Eukaryotic translation initiation factor 3 subunit M / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 42.555832 kDa
SourceSpecies: Rabbit (rabbit)

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Component #41: protein, Eukaryotic translation initiation factor 3 subunit A

ProteinName: Eukaryotic translation initiation factor 3 subunit A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 164.902656 kDa
SourceSpecies: Rabbit (rabbit)

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Component #42: protein, Eukaryotic translation initiation factor 3 subunit C

ProteinName: Eukaryotic translation initiation factor 3 subunit C / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 105.706156 kDa
SourceSpecies: Rabbit (rabbit)

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Component #43: protein, Eukaryotic translation initiation factor 3 subunit D

ProteinName: Eukaryotic translation initiation factor 3 subunit D / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 64.517199 kDa
SourceSpecies: Rabbit (rabbit)

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Component #44: protein, Eukaryotic translation initiation factor 3 subunit H

ProteinName: Eukaryotic translation initiation factor 3 subunit H / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.083531 kDa
SourceSpecies: Rabbit (rabbit)

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Component #45: nucleic-acid, CrPV 5'-UTR IRES

nucleic acidName: CrPV 5'-UTR IRES / Class: RNA
Details: Positions 211 to 220 are only modeled as a polyuridine stretch.
Structure: OTHER / Synthetic: No
Sequence: UUCGAUACCA AGAGCUGGUG UCUGAGGGAU UACGACUCGC GUGGUCGGAC AGCACAUGUU AGUCAUGUAU UAUGGUGUUU CCCAACACGU AUCUUUGCUC UAGUAUUGAA CUUUAGUGAU GAGUGUACUU GGCAUGUACA CCUGAUUAGU UAGCCCUUGU GGAUACGCCA ...Sequence:
UUCGAUACCA AGAGCUGGUG UCUGAGGGAU UACGACUCGC GUGGUCGGAC AGCACAUGUU AGUCAUGUAU UAUGGUGUUU CCCAACACGU AUCUUUGCUC UAGUAUUGAA CUUUAGUGAU GAGUGUACUU GGCAUGUACA CCUGAUUAGU UAGCCCUUGU GGAUACGCCA CUGCCGCUCA GGUACAGUAG GACAUACCCC AAAUAUUGGG UUUUUUUUUU AGAGAAGAAA AUUAGUGGCG AAACGUACGG UUUAUGUCAA AGGAGAAGGU GAUUUUAAUU GCACCUGAAG CAACCCUAGG UCUUCCCUUU GAUGUGAGCU AAUAAGGAGU AACCGAUUCU UACAAUGUGA UCAUGUCUUU UCAACAAACA AAGGAUC
MassTheoretical: 121.094953 kDa
SourceSpecies: Cricket paralysis virus

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Component #46: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #47: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %
Details: Grids were blotted for 2.5s and flash cooled in liquid ethane.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 56.9 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 23444
Details: The microscope was equipped with an energy filter with slits aperture of 20eV, installed before the detector.
3D reconstructionSoftware: RELION / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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