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- EMDB-11320: SARS-CoV-2-Nsp1-40S complex, composite map -

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Basic information

Entry
Database: EMDB / ID: EMD-11320
TitleSARS-CoV-2-Nsp1-40S complex, composite map
Map data
SampleSARS-CoV-2-Nsp1-40S complex, composite map
  • Ribosomal proteinsRibosomal protein
  • SARS-CoV-2-Nsp1
  • nucleic-acidNucleic acid
  • (40S ribosomal protein ...) x 31
  • Ribosomal protein S27aRibosome
  • Receptor of activated protein C kinase 1
  • Non-structural protein 1
  • 60S ribosomal protein L41
  • (ligand) x 2
Function / homology
Function and homology information


positive regulation of respiratory burst involved in inflammatory response / oxidized pyrimidine DNA binding / negative regulation of DNA repair / positive regulation of DNA N-glycosylase activity / response to TNF agonist / positive regulation of base-excision repair / 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 respiratory burst involved in inflammatory response / oxidized pyrimidine DNA binding / negative regulation of DNA repair / positive regulation of DNA N-glycosylase activity / response to TNF agonist / positive regulation of base-excision repair / 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 / response to extracellular stimulus / IRE1-RACK1-PP2A 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 / 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) / erythrocyte development / positive regulation of cyclic-nucleotide phosphodiesterase activity / spindle assembly / TOR signaling / ribosomal small subunit export from nucleus / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of JUN kinase activity / 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 respiratory burst involved in inflammatory response / negative regulation of protein kinase B signaling / small-subunit processome / positive regulation of microtubule polymerization / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / ribosomal small subunit biogenesis / translation initiation factor binding / molecular adaptor activity / positive regulation of DNA repair / gastrulation / polysome / Hsp70 protein binding / laminin binding / positive regulation of cell cycle / erythrocyte differentiation / tubulin binding / translational initiation / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of protein ubiquitination / innate immune response in mucosa / endodeoxyribonuclease activity / polysomal ribosome / MyD88-independent toll-like receptor signaling pathway / mRNA 3'-UTR binding / DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of interleukin-2 production / nucleotide-binding oligomerization domain containing signaling pathway / nucleotide-excision repair, DNA gap filling
Ribosomal protein S3, eukaryotic/archaeal / G-protein beta WD-40 repeat / DPUP/SUD, C-terminal, betacoronavirus / Ribosomal protein S26e / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Non-structural protein NSP1, betacoronavirus / Ribosomal protein S4e / Ribosomal protein S19 conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site ...Ribosomal protein S3, eukaryotic/archaeal / G-protein beta WD-40 repeat / DPUP/SUD, C-terminal, betacoronavirus / Ribosomal protein S26e / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Non-structural protein NSP1, betacoronavirus / Ribosomal protein S4e / Ribosomal protein S19 conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S12/S23 / Ribosomal protein S15P / Ribosomal protein S17, conserved site / Ubiquitin domain / Ubiquitin conserved site / WD40 repeat, conserved site / RNA synthesis protein NSP10, coronavirus / Ribosomal protein S5 / Ribosomal protein S9 / Ribosomal protein S8e, conserved site / Ribosomal protein S8 / Ubiquitin-like domain / Ribosomal protein S4/S9 / Ribosomal protein S19, superfamily / Ribosomal protein S3Ae, conserved site / Ribosomal protein S2, eukaryotic / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein S4, C-terminal domain / Ubiquitin-like domain superfamily / 50S ribosomal protein L30e-like / Ribosomal protein S3, C-terminal / S-adenosyl-L-methionine-dependent methyltransferase / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein SA / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S10 domain / Ribosomal protein S8e / 30s ribosomal protein S13, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S19e / Ribosomal protein S17e / (+) RNA virus helicase core domain / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, N-terminal, betacoronavirus / Ribosomal protein S14 / RNA-directed RNA polymerase, C-terminal domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S6e, conserved site / Ribosomal protein S3, conserved site / Non-structural protein NSP4, C-terminal, coronavirus / Ribosomal protein L23/L15e core domain superfamily / Non-structural protein NSP7, coronavirus / Non-structural protein NSP9, coronavirus / Ribosomal protein L2, domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S6, eukaryotic / Ribosomal protein S4e, central region / Ribosomal protein S4e, N-terminal / Ribosomal protein S5, N-terminal / Peptidase C16, coronavirus / Ribosomal protein S13/S15, N-terminal / WD40/YVTN repeat-like-containing domain superfamily / Peptidase C30, coronavirus / Nucleic acid-binding, OB-fold / Zinc-binding ribosomal protein / Ribosomal protein S13-like, H2TH / RNA polymerase, N-terminal, coronaviral / Non-structural protein 14, coronavirus / Non-structural protein NSP16, coronavirus-like / S15/NS1, RNA-binding / K homology domain superfamily, prokaryotic type / Peptidase S1, PA clan / Non-structural protein NSP8, coronavirus-like / K homology domain-like, alpha/beta / Ribosomal protein S27e / Ribosomal protein S5/S7 / Ribosomal protein S21e, conserved site / Ribosomal protein S15 / Ribosomal protein S7e / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S12e / Ribosomal protein S28e / Ribosomal protein S17/S11 / Ribosomal protein S13, conserved site / WD40-repeat-containing domain / Ribosomal protein S10, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S30 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein L41 / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal S24e conserved site / Ribosomal protein S4, conserved site
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 S28 / 40S ribosomal protein S25 / 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 S28 / 40S ribosomal protein S25 / 40S ribosomal protein S26 / 40S ribosomal protein S30 / 60S ribosomal protein L41 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S21 / Receptor of activated protein C kinase 1 / 40S ribosomal protein S23 / 40S ribosomal protein S18 / 40S ribosomal protein S27 / 40S ribosomal protein S14 / 40S ribosomal protein S19 / 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 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 / 40S ribosomal protein S27a
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSchubert K / Karousis ED / Jomaa A / Scaiola A / Echeverria B / Gurzeler L-A / Leibundgut ML / Thiel V / Muehlemann O / Ban N
Funding support Switzerland, 3 items
OrganizationGrant numberCountry
Swiss National Science Foundation173085 Switzerland
Swiss National Science Foundation182831 Switzerland
Swiss National Science Foundation182341 Switzerland
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation.
Authors: Katharina Schubert / Evangelos D Karousis / Ahmad Jomaa / Alain Scaiola / Blanca Echeverria / Lukas-Adrian Gurzeler / Marc Leibundgut / Volker Thiel / Oliver Mühlemann / Nenad Ban /
Abstract: The SARS-CoV-2 non-structural protein 1 (Nsp1), also referred to as the host shutoff factor, suppresses host innate immune functions. By combining cryo-electron microscopy and biochemistry, we show ...The SARS-CoV-2 non-structural protein 1 (Nsp1), also referred to as the host shutoff factor, suppresses host innate immune functions. By combining cryo-electron microscopy and biochemistry, we show that SARS-CoV-2 Nsp1 binds to the human 40S subunit in ribosomal complexes, including the 43S pre-initiation complex and the non-translating 80S ribosome. The protein inserts its C-terminal domain into the mRNA channel, where it interferes with mRNA binding. We observe translation inhibition in the presence of Nsp1 in an in vitro translation system and in human cells. Based on the high-resolution structure of the 40S-Nsp1 complex, we identify residues of Nsp1 crucial for mediating translation inhibition. We further show that the full-length 5' untranslated region of the genomic viral mRNA stimulates translation in vitro, suggesting that SARS-CoV-2 combines global inhibition of translation by Nsp1 with efficient translation of the viral mRNA to allow expression of viral genes.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJul 7, 2020-
Header (metadata) releaseJul 22, 2020-
Map releaseJul 22, 2020-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.9
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  • Surface view colored by height
  • Surface level: 0.9
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  • Surface view with fitted model
  • Atomic models: PDB-6zoj
  • Surface level: 0.9
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11320.png

Downloads & links

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Map

FileDownload / File: emd_11320.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 560 pix.
= 604.8 Å		1.08 Å/pix.
x 560 pix.
= 604.8 Å		1.08 Å/pix.
x 560 pix.
= 604.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9 / Movie #1: 0.9
Minimum - Maximum-2.2954078 - 6.5481606
Average (Standard dev.)-0.0030948077 (±0.13755026)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 604.80005 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z560560560
origin x/y/z0.0000.0000.000
length x/y/z604.800604.800604.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ250250250
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS560560560
D min/max/mean-2.2956.548-0.003

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Supplemental data

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Sample components

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Entire SARS-CoV-2-Nsp1-40S complex, composite map

EntireName: SARS-CoV-2-Nsp1-40S complex, composite map / Number of components: 41

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Component #1: protein, SARS-CoV-2-Nsp1-40S complex, composite map

ProteinName: SARS-CoV-2-Nsp1-40S complex, composite map / Recombinant expression: No

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Component #2: protein, Ribosomal proteins

ProteinName: Ribosomal proteinsRibosomal protein / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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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: 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 CGGGCGCCGG 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 GCCCUGGCGG AGCGCUGAGA AGACGGUCGA ACUUGACUAU CUAGAGGAAG UAAAAGUCGU AACAAGGUUU CCGUAGGUGA ACCUGCGGAA GGAUCAUUA
MassTheoretical: 602.777875 kDa
SourceSpecies: Homo sapiens (human)

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Component #5: 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 #6: 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 #7: 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 #8: 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 #9: 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 #10: 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 #11: 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 #12: 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 #13: 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 #14: 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 #15: 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 #16: 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 #17: 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 #18: 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 #19: 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 #20: 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 #21: 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 #22: 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 #23: 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 #24: 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 #25: 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 #26: 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 #27: 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 #28: 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 #29: 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 #30: 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 #31: 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 #32: 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 #33: 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 #34: 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 #35: 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 #36: 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 #37: 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 #38: protein, Non-structural protein 1

ProteinName: Non-structural protein 1 / 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)

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Component #39: protein, 60S ribosomal protein L41

ProteinName: 60S ribosomal protein L41 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.473451 kDa
SourceSpecies: Human (human)

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Component #40: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 166 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #41: 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 solutionpH: 7.6
VitrificationCryogen name: OTHER / Temperature: 277.15 K / Humidity: 100 %

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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: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 118765
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

6zoj

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