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- EMDB-3770: Human 40S-eIF2D-re-initiation complex -

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Basic information

Entry
Database: EMDB / ID: EMD-3770
TitleHuman 40S-eIF2D-re-initiation complex
Map data
Samplehuman translation re-initiation complex of eIFD, initiator tRNA and the small ribosomal subunit
  • eIF2D
  • small ribosomal subunit
  • HCV IRES mRNA
  • initiator Met-tRNA-i
  • Eukaryotic translation initiation factor 2D
  • (nucleic-acidNucleic acid) x 3
  • (40S ribosomal protein ...) x 31
  • Ribosomal protein S27aRibosome
  • Receptor of activated protein C kinase 1
  • RIBOSOMAL PROTEIN EL41
  • ligand
Function / homology
Function and homology information


IRES-dependent viral translational initiation / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation / 5.8S rRNA binding / ribosome disassembly / response to extracellular stimulus / positive regulation of Golgi to plasma membrane protein transport / ubiquitin ligase inhibitor activity ...IRES-dependent viral translational initiation / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation / 5.8S rRNA binding / ribosome disassembly / response to extracellular stimulus / positive regulation of Golgi to plasma membrane protein transport / ubiquitin ligase inhibitor activity / negative regulation of RNA splicing / IRE1-RACK1-PP2A complex / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of protein homooligomerization / laminin receptor activity / regulation of cell division / signaling adaptor activity / negative regulation of ubiquitin protein ligase activity / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of base-excision repair / positive regulation of DNA N-glycosylase activity / oxidized pyrimidine DNA binding / response to TNF agonist / negative regulation of DNA repair / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / formation of translation preinitiation complex / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of hydrogen peroxide-induced neuron death / positive regulation of ceramide biosynthetic process / NF-kappaB complex / mammalian oogenesis stage / erythrocyte homeostasis / negative regulation of phagocytosis / negative regulation of Wnt signaling pathway / positive regulation of endodeoxyribonuclease activity / regulation of establishment of cell polarity / pigmentation / protein kinase A binding / activation-induced cell death of T cells / cysteine-type endopeptidase activator activity involved in apoptotic process / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / supercoiled DNA binding / ubiquitin-like protein conjugating enzyme binding / positive regulation of mitochondrial depolarization / translation regulator activity / rescue of stalled ribosome / phagocytic cup / ion channel inhibitor activity / positive regulation of cellular component movement / 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) / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / iron-sulfur cluster binding / fibroblast growth factor binding / stress granule assembly / 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 apoptotic signaling pathway / regulation of translational fidelity / maturation of SSU-rRNA / erythrocyte development / positive regulation of activated T cell proliferation / monocyte chemotaxis / oxidized purine nucleobase lesion DNA N-glycosylase activity / oxidized purine DNA binding / positive regulation of ubiquitin-protein transferase activity / ribosomal small subunit export from nucleus / positive regulation of cyclic-nucleotide phosphodiesterase activity / TOR signaling / negative regulation of protein kinase B signaling / small-subunit processome / negative regulation of ubiquitin-dependent protein catabolic process / regulation of tumor necrosis factor-mediated signaling pathway / T cell proliferation involved in immune response / positive regulation of interleukin-2 production / spindle assembly / ribosomal small subunit biogenesis / SRP-dependent cotranslational protein targeting to membrane / negative regulation of respiratory burst involved in inflammatory response / positive regulation of JUN kinase activity / molecular adaptor activity / gastrulation / translation initiation factor binding / polysome / cellular response to interleukin-4 / positive regulation of microtubule polymerization / innate immune response in mucosa / viral transcription / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / laminin binding / erythrocyte differentiation / polysomal ribosome / mitotic cell cycle checkpoint / positive regulation of cell cycle / tubulin binding / Hsp70 protein binding / positive regulation of intrinsic apoptotic signaling pathway / translation initiation factor activity / negative regulation of peptidyl-serine phosphorylation / mRNA 3'-UTR binding
Ribosomal protein S13-like, H2TH / Ribosomal protein S6, eukaryotic / Ribosomal protein S30 / Ribosomal protein L41 / Ribosomal protein S4e / K homology domain superfamily, prokaryotic type / S15/NS1, RNA-binding / Ribosomal protein S5 / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold ...Ribosomal protein S13-like, H2TH / Ribosomal protein S6, eukaryotic / Ribosomal protein S30 / Ribosomal protein L41 / Ribosomal protein S4e / K homology domain superfamily, prokaryotic type / S15/NS1, RNA-binding / Ribosomal protein S5 / Zinc-binding ribosomal protein / 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 S9 / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S26e / Ribosomal protein L2, domain 2 / WD40/YVTN repeat-like-containing domain superfamily / K homology domain-like, alpha/beta / PUA-like superfamily / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal protein S8 / Ribosomal S24e conserved site / Ubiquitin-like domain / Ribosomal S11, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S27e / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S12/S23 / KOW / Ribosomal protein S13, conserved site / Ribosomal protein S14 / WD40 repeat / Ribosomal protein S3Ae / Ribosomal protein S13 / Ribosomal protein S6e / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S21e / SUI1 domain / Ribosomal protein S3, C-terminal / Ribosomal protein S11 / Ribosomal protein S24e / Ribosomal protein S19e / Ribosomal protein S19/S15 / Ribosomal protein S17e / PUA domain / Ribosomal protein S27a / Ribosomal protein S8e / RNA-binding S4 domain / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / K Homology domain, type 2 / Ribosomal protein S25 / Ribosomal protein S5, C-terminal / Plectin/S10, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S10, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S2 / RNA-binding S4 domain superfamily / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8 superfamily / WD40-repeat-containing domain superfamily / Ribosomal protein S12e / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / SUI1 domain superfamily / SWIB/MDM2 domain superfamily / Ribosomal protein S11 superfamily / PUA domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein S17e, conserved site / Ribosomal protein S19e domain superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S28e / Ribosomal protein S26e superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S17/S11 / S27a-like superfamily / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Eukaryotic translation initiation factor 2D / Ribosomal protein S5/S7 / Eukaryotic translation initiation factor 2D, SUI1 domain / Pre-PUA domain / Ribosomal protein S4, KOW domain / Ribosomal protein S8e subdomain, eukaryotes
40S ribosomal protein S29 / 40S ribosomal protein S24 / 40S ribosomal protein S13 / 40S ribosomal protein S11 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S6 / 40S ribosomal protein S15 / Receptor of activated protein C kinase 1 / 40S ribosomal protein S25 / 40S ribosomal protein S26 ...40S ribosomal protein S29 / 40S ribosomal protein S24 / 40S ribosomal protein S13 / 40S ribosomal protein S11 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S6 / 40S ribosomal protein S15 / Receptor of activated protein C kinase 1 / 40S ribosomal protein S25 / 40S ribosomal protein S26 / 40S ribosomal protein S28 / 40S ribosomal protein S30 / 60S ribosomal protein L41 / 40S ribosomal protein S21 / 40S ribosomal protein S23 / 40S ribosomal protein S18 / 40S ribosomal protein S2 / 40S ribosomal protein S14 / 40S ribosomal protein S27 / 40S ribosomal protein S17 / 40S ribosomal protein SA / 40S ribosomal protein S3 / 40S ribosomal protein S12 / 40S ribosomal protein S19 / Eukaryotic translation initiation factor 2D / 40S ribosomal protein S9 / 40S ribosomal protein S16 / 40S ribosomal protein S5 / 40S ribosomal protein S10 / 40S ribosomal protein S20 / 40S ribosomal protein S3a / 40S ribosomal protein S7 / 40S ribosomal protein S8 / 40S ribosomal protein S15a / Ribosomal protein S27a
Biological speciesHomo sapiens (human) / Hepatitis C virus / Saccharomyces cerevisiae (baker's yeast) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWeisser M / Schaefer T / Leibundgut M / Boehringer D / Aylett CHS / Ban N
CitationJournal: Mol. Cell / Year: 2017
Title: Structural and Functional Insights into Human Re-initiation Complexes.
Authors: Melanie Weisser / Tanja Schäfer / Marc Leibundgut / Daniel Böhringer / Christopher Herbert Stanley Aylett / Nenad Ban /
Abstract: After having translated short upstream open reading frames, ribosomes can re-initiate translation on the same mRNA. This process, referred to as re-initiation, controls the translation of a large ...After having translated short upstream open reading frames, ribosomes can re-initiate translation on the same mRNA. This process, referred to as re-initiation, controls the translation of a large fraction of mammalian cellular mRNAs, many of which are important in cancer. Key ribosomal binding proteins involved in re-initiation are the eukaryotic translation initiation factor 2D (eIF2D) or the homologous complex of MCT-1/DENR. We determined the structures of these factors bound to the human 40S ribosomal subunit in complex with initiator tRNA positioned on an mRNA start codon in the P-site using a combination of cryoelectron microscopy and X-ray crystallography. The structures, supported by biochemical experiments, reveal how eIF2D emulates the function of several canonical translation initiation factors by using three independent, flexibly connected RNA binding domains to simultaneously monitor codon-anticodon interactions in the ribosomal P-site and position the initiator tRNA.
Validation ReportPDB-ID: 5oa3

SummaryFull reportAbout validation report
History
DepositionJun 20, 2017-
Header (metadata) releaseAug 9, 2017-
Map releaseAug 9, 2017-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5oa3
  • Surface level: 0.12
  • 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_3770.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 196 pix.
= 274.4 Å
1.4 Å/pix.
x 196 pix.
= 274.4 Å
1.4 Å/pix.
x 196 pix.
= 274.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.12
Minimum - Maximum-0.64837015 - 0.8811471
Average (Standard dev.)0.007678762 (±0.047832664)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 274.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z196196196
origin x/y/z0.0000.0000.000
length x/y/z274.400274.400274.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS196196196
D min/max/mean-0.6480.8810.008

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Supplemental data

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Additional map: This map was low-pass filtered to 8 Angstroem...

Fileemd_3770_additional.map
AnnotationThis map was low-pass filtered to 8 Angstroem and used for the visualization of secondary structure elements (boxed and map origin re-set to 0).
Projections & Slices
AxesZYX

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Half map: unboxed, unfiltered half-map; origin not re-set.

Fileemd_3770_half_map_1.map
Annotationunboxed, unfiltered half-map; origin not re-set.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: unboxed, unfiltered half-map; origin not re-set.

Fileemd_3770_half_map_2.map
Annotationunboxed, unfiltered half-map; origin not re-set.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire human translation re-initiation complex of eIFD, initiator tRNA a...

EntireName: human translation re-initiation complex of eIFD, initiator tRNA and the small ribosomal subunit
Number of components: 44

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Component #1: protein, human translation re-initiation complex of eIFD, initiat...

ProteinName: human translation re-initiation complex of eIFD, initiator tRNA and the small ribosomal subunit
Recombinant expression: No
MassTheoretical: 1.4 MDa

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Component #2: protein, eIF2D

ProteinName: eIF2D / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, small ribosomal subunit

ProteinName: small ribosomal subunit / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #4: protein, HCV IRES mRNA

ProteinName: HCV IRES mRNA / Recombinant expression: No
SourceSpecies: Hepatitis C virus
Source (engineered)Expression System: Synthetic construct (others)

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Component #5: protein, initiator Met-tRNA-i

ProteinName: initiator Met-tRNA-i / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #6: protein, Eukaryotic translation initiation factor 2D

ProteinName: Eukaryotic translation initiation factor 2D / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 64.788301 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: nucleic-acid, initiator Met-tRNA-i

nucleic acidName: initiator Met-tRNA-i / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AGCGCCGUGG CGCAGUGGAA GCGCGCAGGG CUCAUAACCC UGAUGUCCUC GGAUCGAAAC CGAGCGGCGC UACCA
MassTheoretical: 24.2385 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #8: nucleic-acid, 18S ribosomal RNA

nucleic acidName: 18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: UACCUGGUUG AUCCUGCCAG UAGCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGCG AAUGGCUCAU UAAAUCAGUU AUGGUUCCUU UGGUCGCUCG CUCCUCUCCU ACUUGGAUAA CUGUGGUAAU UCUAGAGCUA ...Sequence:
UACCUGGUUG AUCCUGCCAG UAGCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGCG AAUGGCUCAU UAAAUCAGUU AUGGUUCCUU UGGUCGCUCG CUCCUCUCCU ACUUGGAUAA CUGUGGUAAU UCUAGAGCUA AUACAUGCCG ACGGGCGCUG ACCCCCUUCG CGGGGGGGAU GCGUGCAUUU AUCAGAUCAA AACCAACCCG GUCAGCCCCU CUCCGGCCCC GGCCGGGGGG CGGGCCGCGG CGGCUUUGGU GACUCUAGAU AACCUCGGGC CGAUCGCACG CCCCCCGUGG CGGCGACGAC CCAUUCGAAC GUCUGCCCUA UCAACUUUCG AUGGUAGUCG CCGUGCCUAC CAUGGUGACC ACGGGUGACG GGGAAUCAGG GUUCGAUUCC GGAGAGGGAG CCUGAGAAAC GGCUACCACA UCCAAGGAAG GCAGCAGGCG CGCAAAUUAC CCACUCCCGA CCCGGGGAGG UAGUGACGAA AAAUAACAAU ACAGGACUCU UUCGAGGCCC UGUAAUUGGA AUGAGUCCAC UUUAAAUCCU UUAACGAGGA UCCAUUGGAG GGCAAGUCUG GUGCCAGCAG CCGCGGUAAU UCCAGCUCCA AUAGCGUAUA UUAAAGUUGC UGCAGUUAAA AAGCUCGUAG UUGGAUCUUG GGAGCGGGCG GGCGGUCCGC CGCGAGGCGA GCCACCGCCC GUCCCCGCCC CUUGCCUCUC GGCGCCCCCU CGAUGCUCUU AGCUGAGUGU CCCGCGGGGC CCGAAGCGUU UACUUUGAAA AAAUUAGAGU GUUCAAAGCA GGCCCGAGCC GCCUGGAUAC CGCAGCUAGG AAUAAUGGAA UAGGACCGCG GUUCUAUUUU GUUGGUUUUC GGAACUGAGG CCAUGAUUAA GAGGGACGGC CGGGGGCAUU CGUAUUGCGC CGCUAGAGGU GAAAUUCUUG GACCGGCGCA AGACGGACCA GAGCGAAAGC AUUUGCCAAG AAUGUUUUCA UUAAUCAAGA ACGAAAGUCG GAGGUUCGAA GACGAUCAGA UACCGUCGUA GUUCCGACCA UAAACGAUGC CGACCGGCGA UGCGGCGGCG UUAUUCCCAU GACCCGCCGG GCAGCUUCCG GGAAACCAAA GUCUUUGGGU UCCGGGGGGA GUAUGGUUGC AAAGCUGAAA CUUAAAGGAA UUGACGGAAG GGCACCACCA GGAGUGGAGC CUGCGGCUUA AUUUGACUCA ACACGGGAAA CCUCACCCGG CCCGGACACG GACAGGAUUG ACAGAUUGAU AGCUCUUUCU CGAUUCCGUG GGUGGUGGUG CAUGGCCGUU CUUAGUUGGU GGAGCGAUUU GUCUGGUUAA UUCCGAUAAC GAACGAGACU CUGGCAUGCU AACUAGUUAC GCGACCCCCG AGCGGUCGGC GUCCCCCAAC UUCUUAGAGG GACAAGUGGC GUUCAGCCAC CCGAGAUUGA GCAAUAACAG GUCUGUGAUG CCCUUAGAUG UCCGGGGCUG CACGCGCGCU ACACUGACUG GCUCAGCGUG UGCCUACCCU ACGCCGGCAG GCGCGGGUAA CCCGUUGAAC CCCAUUCGUG AUGGGGAUCG GGGAUUGCAA UUAUUCCCCA UGAACGAGGA AUUCCCAGUA AGUGCGGGUC AUAAGCUUGC GUUGAUUAAG UCCCUGCCCU UUGUACACAC CGCCCGUCGC UACUACCGAU UGGAUGGUUU AGUGAGGCCC UCGGAUCGGC CCCGCCGGGG UCGGCCCACG GCCUGGCGGA GCGCUGAGAA GACGGUCGAA CUUGACUAUC UAGAGGAAGU AAAAGUCGUA ACAAGGUUUC CGUAGGUGAA CCUGCGGAAG GAUCAUUA
MassTheoretical: 602.472688 kDa
SourceSpecies: Human (human)

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Component #9: nucleic-acid, IRES mRNA

nucleic acidName: IRES mRNA / Class: RNA
Details: HCV IRES mRNA (delta domain II mutant, in which domain II of the IRES is replaced with a small stem loop)
Structure: OTHER / Synthetic: No
Sequence: CUCCCCUGCU UCGGCAGGAC CCCCCCUCCC GGGAGAGCCA UAGUGGUCUG CGGAACCGGU GAGUACACCG GAAUUGCCAG GACGACCGGG UCCUUUCUUG GAUAAACCCG CUCAAUGCCU GGAGAUUUGG GCGUGCCCCC GCAAGACUGC UAGCCGAGUA GUGUUGGGUC ...Sequence:
CUCCCCUGCU UCGGCAGGAC 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 AAGAU
MassTheoretical: 88.648414 kDa
SourceSpecies: Hepatitis C virus

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Component #10: protein, 40S ribosomal protein SA

ProteinName: 40S ribosomal protein SA / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.883938 kDa
SourceSpecies: Human (human)

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Component #11: protein, 40S ribosomal protein S3a

ProteinName: 40S ribosomal protein S3a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.002061 kDa
SourceSpecies: Human (human)

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Component #12: protein, 40S ribosomal protein S2

ProteinName: 40S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.376516 kDa
SourceSpecies: Human (human)

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Component #13: protein, 40S ribosomal protein S3

ProteinName: 40S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.729369 kDa
SourceSpecies: Human (human)

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Component #14: protein, 40S ribosomal protein S4, X isoform

ProteinName: 40S ribosomal protein S4, X isoformRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.654869 kDa
SourceSpecies: Human (human)

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Component #15: protein, 40S ribosomal protein S5

ProteinName: 40S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.913453 kDa
SourceSpecies: Human (human)

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Component #16: protein, 40S ribosomal protein S6

ProteinName: 40S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.751906 kDa
SourceSpecies: Human (human)

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Component #17: protein, 40S ribosomal protein S7

ProteinName: 40S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.168914 kDa
SourceSpecies: Human (human)

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Component #18: protein, 40S ribosomal protein S8

ProteinName: 40S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.263387 kDa
SourceSpecies: Human (human)

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Component #19: protein, 40S ribosomal protein S9

ProteinName: 40S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.641564 kDa
SourceSpecies: Human (human)

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Component #20: protein, 40S ribosomal protein S10

ProteinName: 40S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.933846 kDa
SourceSpecies: Human (human)

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Component #21: protein, 40S ribosomal protein S11

ProteinName: 40S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.468826 kDa
SourceSpecies: Human (human)

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Component #22: protein, 40S ribosomal protein S12

ProteinName: 40S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.538987 kDa
SourceSpecies: Human (human)

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Component #23: protein, 40S ribosomal protein S13

ProteinName: 40S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.259389 kDa
SourceSpecies: Human (human)

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Component #24: protein, 40S ribosomal protein S14

ProteinName: 40S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.302772 kDa
SourceSpecies: Human (human)

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Component #25: protein, 40S ribosomal protein S15

ProteinName: 40S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.076207 kDa
SourceSpecies: Human (human)

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Component #26: protein, 40S ribosomal protein S16

ProteinName: 40S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.477377 kDa
SourceSpecies: Human (human)

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Component #27: protein, 40S ribosomal protein S17

ProteinName: 40S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.578156 kDa
SourceSpecies: Human (human)

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Component #28: protein, 40S ribosomal protein S18

ProteinName: 40S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.759777 kDa
SourceSpecies: Human (human)

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Component #29: protein, 40S ribosomal protein S19

ProteinName: 40S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.091562 kDa
SourceSpecies: Human (human)

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Component #30: protein, 40S ribosomal protein S20

ProteinName: 40S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.398763 kDa
SourceSpecies: Human (human)

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Component #31: protein, 40S ribosomal protein S21

ProteinName: 40S ribosomal protein S21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.124389 kDa
SourceSpecies: Human (human)

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Component #32: protein, 40S ribosomal protein S15a

ProteinName: 40S ribosomal protein S15a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.865555 kDa
SourceSpecies: Human (human)

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Component #33: protein, 40S ribosomal protein S23

ProteinName: 40S ribosomal protein S23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.844666 kDa
SourceSpecies: Human (human)

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Component #34: protein, 40S ribosomal protein S24

ProteinName: 40S ribosomal protein S24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.107924 kDa
SourceSpecies: Human (human)

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Component #35: protein, 40S ribosomal protein S25

ProteinName: 40S ribosomal protein S25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.776224 kDa
SourceSpecies: Human (human)

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Component #36: protein, 40S ribosomal protein S26

ProteinName: 40S ribosomal protein S26 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.645794 kDa
SourceSpecies: Human (human)

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Component #37: protein, 40S ribosomal protein S27

ProteinName: 40S ribosomal protein S27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.210843 kDa
SourceSpecies: Human (human)

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Component #38: protein, 40S ribosomal protein S28

ProteinName: 40S ribosomal protein S28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.87894 kDa
SourceSpecies: Human (human)

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Component #39: protein, 40S ribosomal protein S29

ProteinName: 40S ribosomal protein S29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.559625 kDa
SourceSpecies: Human (human)

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Component #40: protein, 40S ribosomal protein S30

ProteinName: 40S ribosomal protein S30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.30248 kDa
SourceSpecies: Human (human)

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Component #41: protein, Ribosomal protein S27a

ProteinName: Ribosomal protein S27aRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.45315 kDa
SourceSpecies: Human (human)

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Component #42: protein, Receptor of activated protein C kinase 1

ProteinName: Receptor of activated protein C kinase 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.857355 kDa
SourceSpecies: Human (human)

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Component #43: protein, RIBOSOMAL PROTEIN EL41

ProteinName: RIBOSOMAL PROTEIN EL41 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.342255 kDa
SourceSpecies: Human (human)

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Component #44: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 3 / 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 solutionSpecimen conc.: 0.11 mg/mL / pH: 7.6
VitrificationCryogen name: OTHER

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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: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 62177
3D reconstructionSoftware: RELION / Resolution: 4.2 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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