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- EMDB-11325: SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-11325
TitleSARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1
Map data
SampleSARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1
  • Human 43S preinitiation ribosome complex
  • SARS-CoV-2 Nsp1
  • (40S ribosomal protein ...) x 31
  • 60S ribosomal protein L41
  • nucleic-acidNucleic acid
  • Ubiquitin-40S ribosomal protein S27a
  • Receptor of activated protein C kinase 1
  • (Eukaryotic translation initiation factor 3 subunit ...) x 11
  • Unknown factor
  • Host translation inhibitor Nsp1
  • ligand
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 / translation reinitiation / positive regulation of mRNA binding / mRNA cap binding / IRES-dependent viral translational initiation / deubiquitinase activity / eukaryotic translation initiation factor 3 complex ...cap-dependent translational initiation / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / positive regulation of mRNA binding / mRNA cap binding / IRES-dependent viral translational initiation / deubiquitinase activity / eukaryotic translation initiation factor 3 complex / multi-eIF complex / cytoplasmic translational initiation / eukaryotic 43S preinitiation complex / positive regulation of DNA N-glycosylase activity / positive regulation of respiratory burst involved in inflammatory response / positive regulation of base-excision repair / negative regulation of DNA repair / response to TNF agonist / oxidized pyrimidine DNA binding / nucleolus organization / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of Golgi to plasma membrane protein transport / NF-kappaB complex / negative regulation of RNA splicing / IRE1-RACK1-PP2A complex / response to extracellular stimulus / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / ubiquitin ligase inhibitor activity / laminin receptor activity / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of cell division / positive regulation of endodeoxyribonuclease activity / oxidized purine DNA binding / negative regulation of endoplasmic reticulum unfolded protein response / protein kinase A binding / negative regulation of hydrogen peroxide-induced neuron death / supercoiled DNA binding / negative regulation of ubiquitin protein ligase activity / regulation of translational initiation / erythrocyte homeostasis / positive regulation of ceramide biosynthetic process / mammalian oogenesis stage / negative regulation of phagocytosis / ubiquitin-like protein conjugating enzyme binding / translation regulator activity / regulation of establishment of cell polarity / signaling adaptor activity / cysteine-type endopeptidase activator activity involved in apoptotic process / negative regulation of Wnt signaling pathway / activation-induced cell death of T cells / positive regulation of T cell receptor signaling pathway / positive regulation of mitochondrial depolarization / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of smoothened signaling pathway / phagocytic cup / ion channel inhibitor activity / iron-sulfur cluster binding / positive regulation of activated T cell proliferation / positive regulation of cellular component movement / fibroblast growth factor binding / rescue of stalled ribosome / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of apoptotic signaling pathway / stress granule assembly / poly(U) RNA binding / monocyte chemotaxis / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of ubiquitin-protein transferase activity / BH3 domain binding / 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) / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / erythrocyte development / positive regulation of cyclic-nucleotide phosphodiesterase activity / spindle assembly / TOR signaling / ribosomal small subunit export from nucleus / positive regulation of JUN kinase activity / regulation of tumor necrosis factor-mediated signaling pathway / maturation of SSU-rRNA / SRP-dependent cotranslational protein targeting to membrane / regulation of translational fidelity / negative regulation of ubiquitin-dependent protein catabolic process / T cell proliferation involved in immune response / negative regulation of protein kinase B signaling / negative regulation of respiratory burst involved in inflammatory response / small-subunit processome / positive regulation of microtubule polymerization / isopeptidase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / translation initiation factor binding / ribosomal small subunit biogenesis / molecular adaptor activity / positive regulation of DNA repair / gastrulation / negative regulation of translational initiation
Zinc-binding ribosomal protein / 40S ribosomal protein S1/3, eukaryotes / Eukaryotic translation initiation factor 3 subunit M / Eukaryotic translation initiation factor 3 subunit I / Ribosomal protein S28e / Ribosomal protein S17/S11 / Eukaryotic translation initiation factor 3 subunit H / Eukaryotic translation initiation factor 3 subunit C / Ribosomal protein S5/S7 / Tetratricopeptide-like helical domain superfamily ...Zinc-binding ribosomal protein / 40S ribosomal protein S1/3, eukaryotes / Eukaryotic translation initiation factor 3 subunit M / Eukaryotic translation initiation factor 3 subunit I / Ribosomal protein S28e / Ribosomal protein S17/S11 / Eukaryotic translation initiation factor 3 subunit H / Eukaryotic translation initiation factor 3 subunit C / Ribosomal protein S5/S7 / Tetratricopeptide-like helical domain superfamily / Eukaryotic translation initiation factor 3 subunit A / 40S ribosomal protein SA / Ribosomal protein S2, eukaryotic / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / P-loop containing nucleoside triphosphate hydrolase / (+) RNA virus helicase core domain / Rpn11/EIF3F, C-terminal / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, N-terminal, betacoronavirus / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Nucleic acid-binding, OB-fold / Eukaryotic translation initiation factor 3 subunit F / Ribosomal protein S28e conserved site / Ribosomal protein S13/S15, N-terminal / Ubiquitin-like domain / Ribosomal protein S4e / Ribosomal protein S5 / Ribosomal protein S9 / RNA synthesis protein NSP10, coronavirus / Proteasome component (PCI) domain / eIF3B, RNA recognition motif / CSN8/PSMD8/EIF3K / Non-structural protein NSP3, nucleic acid-binding (NAR) domain, betacoronavirus / Ribosomal protein S8 / Non-structural protein NSP4, C-terminal, coronavirus / Ribosomal protein S27e / RNA recognition motif domain / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein SA, C-terminal domain / Ribosomal protein S15 / JAB1/MPN/MOV34 metalloenzyme domain / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ubiquitin-like domain superfamily / 50S ribosomal protein L30e-like / Ribosomal protein S12e / S-adenosyl-L-methionine-dependent methyltransferase / Ribosomal protein S19, superfamily / Ribosomal protein S15P / WD40-repeat-containing domain superfamily / Ribosomal protein S10, conserved site / Ubiquitin domain / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ubiquitin conserved site / Ribosomal S11, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Eukaryotic translation initiation factor 3 subunit B / Ribosomal protein S13, conserved site / Eukaryotic translation initiation factor 3 subunit E / Ribosomal protein S14, conserved site / WD40 repeat, conserved site / Ribosomal protein S17e, conserved site / Translation initiation factor 3 complex subunit L / Eukaryotic translation initiation factor 3 subunit E, N-terminal / Ribosomal protein S19e, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S17, conserved site / Armadillo-type fold / Ribosomal protein S4/S9 / Translation initiation factor, beta propellor-like domain / DPUP/SUD, C-terminal, betacoronavirus / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Non-structural protein NSP1, betacoronavirus / Ribosomal protein L23/L15e core domain superfamily / Peptidase C16, coronavirus / Ribosomal protein S5, N-terminal / Ribosomal protein S19 conserved site / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Ribosomal protein S6, eukaryotic / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L2, domain 2 / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, coronavirus / G-protein beta WD-40 repeat
40S ribosomal protein S6 / 40S ribosomal protein S24 / 40S ribosomal protein S15 / 40S ribosomal protein S29 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S11 / 40S ribosomal protein S13 / 40S ribosomal protein S26 / 40S ribosomal protein S25 / 40S ribosomal protein S21 ...40S ribosomal protein S6 / 40S ribosomal protein S24 / 40S ribosomal protein S15 / 40S ribosomal protein S29 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S11 / 40S ribosomal protein S13 / 40S ribosomal protein S26 / 40S ribosomal protein S25 / 40S ribosomal protein S21 / 40S ribosomal protein S28 / 40S ribosomal protein S30 / 60S ribosomal protein L41 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S23 / Receptor of activated protein C kinase 1 / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit M / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit K / 40S ribosomal protein S18 / 40S ribosomal protein S7 / 40S ribosomal protein S14 / 40S ribosomal protein S19 / Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit H / 40S ribosomal protein S17 / 40S ribosomal protein SA / Replicase polyprotein 1ab / 40S ribosomal protein S2 / 40S ribosomal protein S3 / 40S ribosomal protein S12 / 40S ribosomal protein S27 / 40S ribosomal protein S16 / 40S ribosomal protein S9 / 40S ribosomal protein S5 / 40S ribosomal protein S10 / Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 3 subunit E / 40S ribosomal protein S20 / 40S ribosomal protein S3a / 40S ribosomal protein S8 / 40S ribosomal protein S15a / Eukaryotic translation initiation factor 3 subunit L
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsThoms M / Buschauer R / Ameismeier M / Denk T / Kratzat H / Mackens-Kiani T / Cheng J / Berninghausen O / Becker T / Beckmann R
Funding support Germany, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB/TRR-174 Germany
German Research Foundation (DFG)BE1814/1-1 Germany
German Research Foundation (DFG)BE1814/15-1 Germany
CitationJournal: Science / Year: 2020
Title: Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Authors: Matthias Thoms / Robert Buschauer / Michael Ameismeier / Lennart Koepke / Timo Denk / Maximilian Hirschenberger / Hanna Kratzat / Manuel Hayn / Timur Mackens-Kiani / Jingdong Cheng / Jan H ...Authors: Matthias Thoms / Robert Buschauer / Michael Ameismeier / Lennart Koepke / Timo Denk / Maximilian Hirschenberger / Hanna Kratzat / Manuel Hayn / Timur Mackens-Kiani / Jingdong Cheng / Jan H Straub / Christina M Stürzel / Thomas Fröhlich / Otto Berninghausen / Thomas Becker / Frank Kirchhoff / Konstantin M J Sparrer / Roland Beckmann /
Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current coronavirus disease 2019 (COVID-19) pandemic. A major virulence factor of SARS-CoVs is the ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current coronavirus disease 2019 (COVID-19) pandemic. A major virulence factor of SARS-CoVs is the nonstructural protein 1 (Nsp1), which suppresses host gene expression by ribosome association. Here, we show that Nsp1 from SARS-CoV-2 binds to the 40 ribosomal subunit, resulting in shutdown of messenger RNA (mRNA) translation both in vitro and in cells. Structural analysis by cryo-electron microscopy of in vitro-reconstituted Nsp1-40 and various native Nsp1-40 and -80 complexes revealed that the Nsp1 C terminus binds to and obstructs the mRNA entry tunnel. Thereby, Nsp1 effectively blocks retinoic acid-inducible gene I-dependent innate immune responses that would otherwise facilitate clearance of the infection. Thus, the structural characterization of the inhibitory mechanism of Nsp1 may aid structure-based drug design against SARS-CoV-2.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJul 7, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateSep 16, 2020-
Current statusSep 16, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zon
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11325.png

Downloads & links

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Map

FileDownload / File: emd_11325.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 381.24 Å		1.06 Å/pix.
x 360 pix.
= 381.24 Å		1.06 Å/pix.
x 360 pix.
= 381.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.07535854 - 0.29902884
Average (Standard dev.)0.0006338182 (±0.008944825)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 381.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z381.240381.240381.240
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0750.2990.001

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Supplemental data

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Sample components

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Entire SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome compl...

EntireName: SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1
Number of components: 52

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Component #1: protein, SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribos...

ProteinName: SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1
Recombinant expression: No

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Component #2: protein, Human 43S preinitiation ribosome complex

ProteinName: Human 43S preinitiation ribosome complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #3: protein, SARS-CoV-2 Nsp1

ProteinName: SARS-CoV-2 Nsp1 / Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #4: protein, 40S ribosomal protein SA

ProteinName: 40S ribosomal protein SA / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.883938 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #5: protein, 40S ribosomal protein S3a

ProteinName: 40S ribosomal protein S3a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.002061 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #6: protein, 40S ribosomal protein S2

ProteinName: 40S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.376516 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #7: protein, 40S ribosomal protein S26

ProteinName: 40S ribosomal protein S26 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.047532 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #8: 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: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #9: protein, 60S ribosomal protein L41

ProteinName: 60S ribosomal protein L41 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.473451 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #10: protein, 40S ribosomal protein S6

ProteinName: 40S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.751906 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #11: protein, 40S ribosomal protein S7

ProteinName: 40S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.168914 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #12: protein, 40S ribosomal protein S8

ProteinName: 40S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.263387 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #13: protein, 40S ribosomal protein S9

ProteinName: 40S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.641564 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #14: protein, 40S ribosomal protein S11

ProteinName: 40S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.468826 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #15: protein, 40S ribosomal protein S13

ProteinName: 40S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.259389 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #16: protein, 40S ribosomal protein S14

ProteinName: 40S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.302772 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #17: protein, 40S ribosomal protein S21

ProteinName: 40S ribosomal protein S21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.124389 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #18: protein, 40S ribosomal protein S15a

ProteinName: 40S ribosomal protein S15a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.865555 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #19: protein, 40S ribosomal protein S23

ProteinName: 40S ribosomal protein S23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.844666 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #20: protein, 40S ribosomal protein S24

ProteinName: 40S ribosomal protein S24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.463333 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #21: protein, 40S ribosomal protein S27

ProteinName: 40S ribosomal protein S27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.480186 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #22: protein, 40S ribosomal protein S30

ProteinName: 40S ribosomal protein S30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.668938 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #23: 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 CCCUGGCGGA GCGCUGAGAA GACGGUCGAA CUUGACUAUC UAGAGGAAGU AAAAGUCGUA ACAAGGUUUC CGUAGGUGAA CCUGCGGAAG GAUCAUUA
MassTheoretical: 602.432625 kDa
SourceSpecies: Homo sapiens (human)

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Component #24: protein, 40S ribosomal protein S17

ProteinName: 40S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.578156 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #25: protein, 40S ribosomal protein S16

ProteinName: 40S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.477377 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #26: protein, 40S ribosomal protein S3

ProteinName: 40S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.729369 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #27: protein, 40S ribosomal protein S5

ProteinName: 40S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.913453 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #28: protein, 40S ribosomal protein S10

ProteinName: 40S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.933846 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #29: protein, 40S ribosomal protein S12

ProteinName: 40S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.538987 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #30: protein, 40S ribosomal protein S15

ProteinName: 40S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.076207 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #31: protein, 40S ribosomal protein S18

ProteinName: 40S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.759777 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #32: protein, 40S ribosomal protein S19

ProteinName: 40S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.091562 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #33: protein, 40S ribosomal protein S20

ProteinName: 40S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.398763 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #34: protein, 40S ribosomal protein S25

ProteinName: 40S ribosomal protein S25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.776224 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

+
Component #35: protein, 40S ribosomal protein S28

ProteinName: 40S ribosomal protein S28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.855052 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

+
Component #36: protein, 40S ribosomal protein S29

ProteinName: 40S ribosomal protein S29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.690821 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

+
Component #37: protein, Ubiquitin-40S ribosomal protein S27a

ProteinName: Ubiquitin-40S ribosomal protein S27a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.004041 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

+
Component #38: protein, Receptor of activated protein C kinase 1

ProteinName: Receptor of activated protein C kinase 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.115652 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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

ProteinName: Eukaryotic translation initiation factor 3 subunit I / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.543773 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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

ProteinName: Eukaryotic translation initiation factor 3 subunit B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 92.593414 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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

ProteinName: Eukaryotic translation initiation factor 3 subunit A,Eukaryotic translation initiation factor 3 subunit A
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 79.249359 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

+
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: 105.503945 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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

ProteinName: Eukaryotic translation initiation factor 3 subunit E / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.281633 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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

ProteinName: Eukaryotic translation initiation factor 3 subunit F / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.593645 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

+
Component #45: protein, Eukaryotic translation initiation factor 3 subunit H

ProteinName: Eukaryotic translation initiation factor 3 subunit H / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.979277 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

+
Component #46: protein, Eukaryotic translation initiation factor 3 subunit K

ProteinName: Eukaryotic translation initiation factor 3 subunit K / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.083619 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

+
Component #47: protein, Eukaryotic translation initiation factor 3 subunit L

ProteinName: Eukaryotic translation initiation factor 3 subunit L / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 66.803734 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

+
Component #48: 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: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

+
Component #49: protein, Eukaryotic translation initiation factor 3 subunit D

ProteinName: Eukaryotic translation initiation factor 3 subunit D / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 64.060758 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

+
Component #50: protein, Unknown factor

ProteinName: Unknown factor / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.656196 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

+
Component #51: protein, Host translation inhibitor Nsp1

ProteinName: Host translation inhibitor Nsp1 / Details: Host translation inhibitor Nsp1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.801287 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

+
Component #52: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

-
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: 44.8 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 13928
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Output model

6zon

+
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