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- EMDB-11321: SARS-CoV-2-Nsp1-40S complex, focused on body -

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Basic information

Entry
Database: EMDB / ID: EMD-11321
TitleSARS-CoV-2-Nsp1-40S complex, focused on body
Map data
SampleSARS-CoV-2-Nsp1-40S, focused on body:
Ribosomal proteinsRibosomal protein / SARS-CoV-2-Nsp1-40S / nucleic-acidNucleic acid / (40S ribosomal protein ...) x 19 / Non-structural protein 1 / 60S ribosomal protein L41 / (ligand) x 2
Function / homology
Function and homology information


negative regulation of RNA splicing / ubiquitin ligase inhibitor activity / laminin receptor activity / cytoplasmic side of rough endoplasmic reticulum membrane / negative regulation of ubiquitin protein ligase activity / erythrocyte homeostasis / mammalian oogenesis stage / translation regulator activity / activation-induced cell death of T cells / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...negative regulation of RNA splicing / ubiquitin ligase inhibitor activity / laminin receptor activity / cytoplasmic side of rough endoplasmic reticulum membrane / negative regulation of ubiquitin protein ligase activity / erythrocyte homeostasis / mammalian oogenesis stage / translation regulator activity / activation-induced cell death of T cells / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / fibroblast growth factor binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / stress granule assembly / poly(U) RNA binding / positive regulation of ubiquitin-protein transferase activity / 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 / TOR signaling / maturation of SSU-rRNA / SRP-dependent cotranslational protein targeting to membrane / negative regulation of ubiquitin-dependent protein catabolic process / T cell proliferation involved in immune response / small-subunit processome / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / translation initiation factor binding / ribosomal small subunit biogenesis / gastrulation / polysome / laminin binding / positive regulation of cell cycle / erythrocyte differentiation / translational initiation / innate immune response in mucosa / polysomal ribosome / mRNA 3'-UTR binding / modulation by virus of host autophagy / maintenance of translational fidelity / positive regulation of translational fidelity / microtubule organizing center / mRNA methylation / RNA phosphodiester bond hydrolysis, exonucleolytic / suppression by virus of host translation / ISG15-specific protease activity / suppression by virus of host type I interferon production / small ribosomal subunit rRNA binding / suppression by virus of host toll-like receptor signaling pathway / neural tube closure / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / induction by virus of catabolism of host mRNA / SARS coronavirus main proteinase / cytoplasmic viral factory / cytoplasmic ribonucleoprotein granule / suppression by virus of host ISG15 activity / response to virus / protein K48-linked deubiquitination / positive regulation of translation / rough endoplasmic reticulum / 3'-5'-exoribonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / suppression by virus of host IRF3 activity / exonuclease activity / modulation by virus of host protein ubiquitination / suppression by virus of host NF-kappaB transcription factor activity / mRNA 5'-UTR binding / transcription, RNA-templated / protein K63-linked deubiquitination / placenta development / rRNA processing / viral genome replication / positive stranded viral RNA replication / protein autoprocessing / cytoplasmic translation / G1/S transition of mitotic cell cycle / viral transcription / Transferases; Transferring one-carbon groups; Methyltransferases / suppression by virus of host TRAF activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / helicase activity / host cell membrane / virus receptor activity / ubiquitinyl hydrolase 1 / cytosolic large ribosomal subunit / cell body / cysteine-type peptidase activity / DNA helicase / ribosome binding / methyltransferase activity / DNA helicase activity / single-stranded RNA binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / thiol-dependent deubiquitinase / cytosolic small ribosomal subunit / ribonucleoprotein complex / small ribosomal subunit / glucose homeostasis / host cell perinuclear region of cytoplasm / viral protein processing / T cell differentiation in thymus
Peptidase C16, coronavirus / Ribosomal protein S4, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal S24e conserved site / Non-structural protein NSP8, coronavirus-like / Ribosomal protein S3Ae, conserved site ...Peptidase C16, coronavirus / Ribosomal protein S4, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal S24e conserved site / Non-structural protein NSP8, coronavirus-like / Ribosomal protein S3Ae, conserved site / 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 S21e, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S7e / Ribosomal protein S2, flavodoxin-like domain superfamily / 40S ribosomal protein SA / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S2, eukaryotic / P-loop containing nucleoside triphosphate hydrolase / (+) RNA virus helicase core domain / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, N-terminal, betacoronavirus / Ribosomal protein S15P / Ribosomal protein S8e, conserved site / Ribosomal protein S4/S9 / Ribosomal protein S5, N-terminal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Non-structural protein NSP1, betacoronavirus / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S17, conserved site / RNA synthesis protein NSP10, coronavirus / Ribosomal protein S17/S11 / Ribosomal protein S15 / S-adenosyl-L-methionine-dependent methyltransferase / Peptidase S1, PA clan / Ribosomal protein S5, eukaryotic/archaeal / KOW / Ribosomal protein S12/S23 / Ribosomal protein S30 / Ribosomal protein L41 / Peptidase C30, coronavirus / S15/NS1, RNA-binding / Ribosomal protein S2, eukaryotic/archaeal / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronaviral / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Ribosomal protein S13/S15, N-terminal / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S27e / Ribosomal protein S6e / Ribosomal protein S8 / Ribosomal protein S5 / Ribosomal protein S4e / Ribosomal protein S26e / Ribosomal protein S8e / RNA-directed RNA polymerase, C-terminal domain / Ribosomal protein S17e / Ribosomal protein S3Ae / Ribosomal protein S5, C-terminal / Ribosomal protein S2 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S21e / Ribosomal protein S11 / Ribosomal protein S24e / Macro domain / RNA-binding S4 domain / Ribosomal protein S17, archaeal/eukaryotic / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP15, middle domain superfamily / Non-structural protein NSP4, C-terminal superfamily, coronavirus / RNA-binding S4 domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Ribosomal protein S4, KOW domain / Non-structural protein NSP7 superfamily, coronavirus / Replicase polyprotein, nucleic acid-binding domain superfamily / Endoribonuclease EndoU-like / DNA/RNA polymerase superfamily / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP1 superfamily, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Peptidase C30, domain 3, coronavirus / Coronavirus replicase NSP15, middle domain / Polyprotein cleavage domain PL2pro superfamily, coronavirus / 40S ribosomal protein S4, C-terminal domain / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Yro2-like, 7TM domain / Ribosomal protein S4e, central domain superfamily / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Ribosomal protein S26e superfamily
40S ribosomal protein S17 / 40S ribosomal protein S23 / 60S ribosomal protein L41 / 40S ribosomal protein S30 / 40S ribosomal protein S26 / 40S ribosomal protein S24 / 40S ribosomal protein S6 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S11 / 40S ribosomal protein S13 ...40S ribosomal protein S17 / 40S ribosomal protein S23 / 60S ribosomal protein L41 / 40S ribosomal protein S30 / 40S ribosomal protein S26 / 40S ribosomal protein S24 / 40S ribosomal protein S6 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S11 / 40S ribosomal protein S13 / 40S ribosomal protein S14 / 40S ribosomal protein SA / 40S ribosomal protein S15a / 40S ribosomal protein S8 / 40S ribosomal protein S7 / 40S ribosomal protein S3a / 40S ribosomal protein S9 / 40S ribosomal protein S27 / 40S ribosomal protein S2 / Replicase polyprotein 1ab / 40S ribosomal protein S21
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 M / 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 29, 2020-
Map releaseJul 29, 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: 0.8
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  • Atomic models: PDB-6zok
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zok
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Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11321.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
Contour LevelBy AUTHOR: 0.8 / Movie #1: 0.8
Minimum - Maximum-3.4848747 - 7.1133537
Average (Standard dev.)-0.0015249234 (±0.1427928)
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/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS560560560
D min/max/mean-3.4857.113-0.002

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Supplemental data

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Segmentation: #1

Fileemd_11321_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_11321_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_11321_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire SARS-CoV-2-Nsp1-40S, focused on body

EntireName: SARS-CoV-2-Nsp1-40S, focused on body / Number of components: 27

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Component #1: protein, SARS-CoV-2-Nsp1-40S, focused on body

ProteinName: SARS-CoV-2-Nsp1-40S, focused on body / 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-Nsp1-40S

ProteinName: SARS-CoV-2-Nsp1-40S / 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: Human (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 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 #9: 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 #10: 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 #11: 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 #12: 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 #13: 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 #14: 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 #15: 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 #16: 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 #17: 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 #18: 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 #19: 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 #20: 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 #21: 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 #22: 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 #23: 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 #24: 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 #25: 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 #26: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 109 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #27: ligand, ZINC ION

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

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.6
VitrificationCryogen name: OTHER

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 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

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