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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 / mRNA cap binding / positive regulation of mRNA binding / IRES-dependent viral translational initiation / multi-eIF complex / negative regulation of DNA repair ...cap-dependent translational initiation / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / mRNA cap binding / positive regulation of mRNA binding / IRES-dependent viral translational initiation / multi-eIF complex / negative regulation of DNA repair / response to TNF agonist / positive regulation of base-excision repair / positive regulation of DNA N-glycosylase activity / oxidized pyrimidine DNA binding / eukaryotic translation initiation factor 3 complex / cytoplasmic translational initiation / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / eukaryotic 43S preinitiation complex / NF-kappaB complex / positive regulation of Golgi to plasma membrane protein transport / ubiquitin ligase inhibitor activity / response to extracellular stimulus / negative regulation of RNA splicing / IRE1-RACK1-PP2A complex / cytoplasmic side of rough endoplasmic reticulum membrane / eukaryotic 48S preinitiation complex / laminin receptor activity / formation of cytoplasmic translation initiation complex / regulation of cell division / positive regulation of endodeoxyribonuclease activity / oxidized purine DNA binding / protein kinase A binding / signaling adaptor activity / negative regulation of endoplasmic reticulum unfolded protein response / negative regulation of ubiquitin protein ligase activity / supercoiled DNA binding / negative regulation of hydrogen peroxide-induced neuron death / ubiquitin-like protein conjugating enzyme binding / positive regulation of ceramide biosynthetic process / erythrocyte homeostasis / regulation of translational initiation / negative regulation of phagocytosis / regulation of establishment of cell polarity / negative regulation of Wnt signaling pathway / pigmentation / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of T cell receptor signaling pathway / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / positive regulation of mitochondrial depolarization / phagocytic cup / rescue of stalled ribosome / DNA-(apurinic or apyrimidinic site) lyase / positive regulation of activated T cell proliferation / ion channel inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of cellular component movement / fibroblast growth factor binding / iron-sulfur cluster 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) / stress granule assembly / positive regulation of apoptotic signaling pathway / poly(U) RNA binding / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / monocyte chemotaxis / positive regulation of interleukin-2 production / positive regulation of ubiquitin-protein transferase activity / maturation of SSU-rRNA / BH3 domain binding / regulation of translational fidelity / positive regulation of cyclic-nucleotide phosphodiesterase activity / spindle assembly / ribosomal small subunit export from nucleus / TOR signaling / positive regulation of JUN kinase activity / regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of protein kinase B signaling / small-subunit processome / negative regulation of ubiquitin-dependent protein catabolic process / gastrulation / SRP-dependent cotranslational protein targeting to membrane / negative regulation of respiratory burst involved in inflammatory response / positive regulation of microtubule polymerization / ribosomal small subunit biogenesis / SARS coronavirus main proteinase / induction by virus of catabolism of host mRNA / polysome / translation initiation factor binding / molecular adaptor activity / suppression by virus of host ISG15 activity / exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / negative regulation of translational initiation / positive regulation of DNA repair / Hsp70 protein binding
Ribosomal protein S4/S9, N-terminal / Ribosomal protein L2, domain 2 / Ribosomal S24e conserved site / Ribosomal protein S4, conserved site / WD40-repeat-containing domain / Ribosomal protein S21e / 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 S4/S9, N-terminal / Ribosomal protein L2, domain 2 / Ribosomal S24e conserved site / Ribosomal protein S4, conserved site / WD40-repeat-containing domain / Ribosomal protein S21e / 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 / Non-structural protein NSP8, coronavirus-like / Non-structural protein NSP7, coronavirus / in:ipr014827: / Non-structural protein NSP9, coronavirus / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S2, conserved site / Ribosomal protein S6, eukaryotic / Translation initiation factor, beta propellor-like domain / Ribosomal protein S4e, central region / Ribosomal protein S4e, N-terminal / Ribosomal protein S5, N-terminal / Ribosomal protein L23/L15e core domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein S13/S15, N-terminal / Nucleic acid-binding, OB-fold / Tetratricopeptide-like helical domain superfamily / Eukaryotic translation initiation factor 3 subunit B / Zinc-binding ribosomal protein / Ribosomal S11, conserved site / Ribosomal protein S5, N-terminal, conserved site / RNA polymerase, N-terminal, coronaviral / WD40 repeat, conserved site / Ribosomal protein S4/S9 / DPUP/SUD, C-terminal, betacoronavirus / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Non-structural protein NSP1, betacoronavirus / Ribosomal protein S19 conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ribosomal protein S17, conserved site / Ubiquitin domain / Ubiquitin conserved site / Translation initiation factor 3 complex subunit L / Ribosomal protein S4e, N-terminal, conserved site / Eukaryotic translation initiation factor 3 subunit E, N-terminal / RNA synthesis protein NSP10, coronavirus / Ribosomal protein S8e, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S13-like, H2TH / Non-structural protein NSP15, coronavirus / Ribosomal protein S19, superfamily / Ribosomal protein S5 / Ribosomal protein S17/S11 / Ribosomal protein S28e / RNA recognition motif domain / Ribosomal protein S12e / Ribosomal protein S7e / JAB1/MPN/MOV34 metalloenzyme domain / Ribosomal protein S15 / Ribosomal protein S27e / Ubiquitin-like domain / Ribosomal protein S8 / Proteasome component (PCI) domain / Ribosomal protein S9 / Ribosomal protein S4e / Ribosomal protein S11 / Ribosomal protein S26e / Ribosomal protein S8e / Ribosomal protein S14 / Ribosomal protein S17e / Ribosomal protein S19e / Ribosomal protein S3, C-terminal / Ribosomal protein S6e / Ribosomal protein S3Ae / WD40 repeat / Ribosomal protein S10 / Ribosomal protein S2 / Ribosomal protein S13 / Ribosomal protein S5/S7 / Ribosomal protein S24e / Non-structural protein NSP16, coronavirus-like / Ribosomal protein S5/S7, eukaryotic/archaeal / Eukaryotic translation initiation factor 3 subunit K / S15/NS1, RNA-binding / K homology domain superfamily, prokaryotic type / Peptidase S1, PA clan / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Peptidase C30, coronavirus / Ribosomal protein L41 / Eukaryotic translation initiation factor 3 subunit D
Eukaryotic translation initiation factor 3 subunit K / 40S ribosomal protein S26 / 40S ribosomal protein S29 / 40S ribosomal protein S13 / 40S ribosomal protein S11 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S6 / 40S ribosomal protein S15 / 40S ribosomal protein S24 / 40S ribosomal protein S25 ...Eukaryotic translation initiation factor 3 subunit K / 40S ribosomal protein S26 / 40S ribosomal protein S29 / 40S ribosomal protein S13 / 40S ribosomal protein S11 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S6 / 40S ribosomal protein S15 / 40S ribosomal protein S24 / 40S ribosomal protein S25 / 40S ribosomal protein S28 / Eukaryotic translation initiation factor 3 subunit C / 40S ribosomal protein S30 / 60S ribosomal protein L41 / 40S ribosomal protein S23 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S21 / 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 / 40S ribosomal protein S18 / 40S ribosomal protein S12 / 40S ribosomal protein S14 / 40S ribosomal protein S27 / 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 S19 / 40S ribosomal protein S9 / 40S ribosomal protein S16 / 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 S7 / 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: SARS-CoV-2 is the causative agent of the current COVID-19 pandemic. A major virulence factor of SARS-CoVs is the nonstructural protein 1 (Nsp1) which suppresses host gene expression by ribosome ...SARS-CoV-2 is the causative agent of the current 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 40S ribosomal subunit, resulting in shutdown of mRNA translation both in vitro and in cells. Structural analysis by cryo-electron microscopy (cryo-EM) of in vitro reconstituted Nsp1-40S and various native Nsp1-40S and -80S complexes revealed that the Nsp1 C terminus binds to and obstructs the mRNA entry tunnel. Thereby, Nsp1 effectively blocks RIG-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 ReportPDB-ID: 6zon

SummaryFull reportAbout validation report
History
DepositionJul 7, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateJul 29, 2020-
Current statusJul 29, 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
  • Download
  • 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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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
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)

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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

+
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