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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 DNA N-glycosylase activity / negative regulation of DNA repair / response to TNF agonist / positive regulation of base-excision repair / oxidized pyrimidine DNA binding / positive regulation of respiratory burst involved in inflammatory response / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / nucleolus organization / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / mammalian oogenesis stage ...positive regulation of DNA N-glycosylase activity / negative regulation of DNA repair / response to TNF agonist / positive regulation of base-excision repair / oxidized pyrimidine DNA binding / positive regulation of respiratory burst involved in inflammatory response / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / nucleolus organization / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / mammalian oogenesis stage / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation / NF-kappaB complex / positive regulation of Golgi to plasma membrane protein transport / IRE1-RACK1-PP2A complex / negative regulation of RNA splicing / response to extracellular stimulus / ubiquitin ligase inhibitor activity / laminin receptor activity / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of endodeoxyribonuclease activity / regulation of cell division / oxidized purine DNA binding / activation-induced cell death of T cells / negative regulation of endoplasmic reticulum unfolded protein response / supercoiled DNA binding / negative regulation of hydrogen peroxide-induced neuron death / protein kinase A binding / positive regulation of ceramide biosynthetic process / negative regulation of ubiquitin protein ligase activity / erythrocyte homeostasis / negative regulation of phagocytosis / ubiquitin-like protein conjugating enzyme binding / signaling adaptor activity / regulation of establishment of cell polarity / negative regulation of Wnt signaling pathway / translation regulator activity / pigmentation / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of T cell receptor signaling pathway / positive regulation of mitochondrial depolarization / phagocytic cup / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ion channel inhibitor activity / positive regulation of activated T cell proliferation / erythrocyte development / rescue of stalled ribosome / positive regulation of cellular component movement / fibroblast growth factor binding / iron-sulfur cluster binding / positive regulation of apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / stress granule assembly / DNA-(apurinic or apyrimidinic site) lyase / monocyte chemotaxis / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / T cell proliferation involved in immune response / positive regulation of ubiquitin-protein transferase activity / BH3 domain binding / positive regulation of cyclic-nucleotide phosphodiesterase 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) / spindle assembly / TOR signaling / positive regulation of JUN kinase activity / regulation of tumor necrosis factor-mediated signaling pathway / ribosomal small subunit export from nucleus / SRP-dependent cotranslational protein targeting to membrane / positive regulation of interleukin-2 production / negative regulation of protein kinase B signaling / maturation of SSU-rRNA / negative regulation of ubiquitin-dependent protein catabolic process / regulation of translational fidelity / gastrulation / negative regulation of respiratory burst involved in inflammatory response / positive regulation of microtubule polymerization / small-subunit processome / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / polysome / viral transcription / translation initiation factor binding / ribosomal small subunit biogenesis / molecular adaptor activity / positive regulation of DNA repair / Hsp70 protein binding / induction by virus of catabolism of host mRNA / erythrocyte differentiation / laminin binding / SARS coronavirus main proteinase / mitotic cell cycle checkpoint / suppression by virus of host ISG15 activity / cellular response to interleukin-4 / positive regulation of cell cycle / omega peptidase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / tubulin binding / translational initiation / innate immune response in mucosa / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / suppression by virus of host NF-kappaB transcription factor activity / exonuclease activity
KOW / Ribosomal protein L2, domain 2 / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal S24e conserved site / Ribosomal protein S4, conserved site / WD40-repeat-containing domain / K homology domain-like, alpha/beta / WD40/YVTN repeat-like-containing domain superfamily / Non-structural protein NSP8, coronavirus-like ...KOW / Ribosomal protein L2, domain 2 / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal S24e conserved site / Ribosomal protein S4, conserved site / WD40-repeat-containing domain / K homology domain-like, alpha/beta / WD40/YVTN repeat-like-containing domain superfamily / Non-structural protein NSP8, coronavirus-like / Non-structural protein NSP7, coronavirus / Non-structural protein NSP9, coronavirus / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S6, eukaryotic / Ribosomal protein S4e, central region / Ribosomal protein S4e, N-terminal / Ribosomal protein S5, N-terminal / Peptidase C16, coronavirus / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein S13/S15, N-terminal / Nucleic acid-binding, OB-fold / Zinc-binding ribosomal protein / Ribosomal protein S13-like, H2TH / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S10, conserved site / Non-structural protein NSP14, coronavirus / Ribosomal protein S17, conserved site / Ribosomal protein S15P / 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 / Ubiquitin domain / Ribosomal protein S13, conserved site / Ubiquitin conserved site / WD40 repeat, conserved site / 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 S12/S23 / Ribosomal protein S19e, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S14, conserved site / RNA polymerase, N-terminal, coronaviral / Non-structural protein NSP16, coronavirus-like / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein S2 / Ribosomal protein S13 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S21e / Ribosomal protein S11 / Ribosomal protein S24e / Ribosomal protein S19/S15 / Macro domain / Ribosomal protein S27a / RNA-binding S4 domain / K Homology domain, type 2 / WD40 repeat / Ribosomal protein S25 / Ribosomal protein S5, C-terminal / Plectin/S10, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S10 / Ribosomal protein S3Ae / S15/NS1, RNA-binding / Ribosomal protein S15 / K homology domain superfamily, prokaryotic type / Peptidase S1, PA clan / Peptidase C30, coronavirus / Ribosomal protein L41 / Ribosomal protein S30 / Ribosomal protein S5/S7 / Ribosomal protein S17/S11 / Ribosomal protein S28e / Ribosomal protein S12e / Ribosomal protein S7e / Ribosomal protein S27e / Ribosomal protein S6e / Ubiquitin-like domain / Ribosomal protein S8 / Ribosomal protein S9 / Ribosomal protein S5 / Ribosomal protein S4e / Ribosomal protein S26e
40S ribosomal protein S24 / 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 S21 / 40S ribosomal protein S25 / 40S ribosomal protein S26 ...40S ribosomal protein S24 / 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 S21 / 40S ribosomal protein S25 / 40S ribosomal protein S26 / 40S ribosomal protein S28 / 40S ribosomal protein S30 / 60S ribosomal protein L41 / Receptor of activated protein C kinase 1 / 40S ribosomal protein S23 / 40S ribosomal protein S18 / 40S ribosomal protein S2 / 40S ribosomal protein S14 / 40S ribosomal protein S27 / 40S ribosomal protein S17 / 40S ribosomal protein SA / Replicase polyprotein 1ab / 40S ribosomal protein S3 / 40S ribosomal protein S12 / 40S ribosomal protein S19 / 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 ReportPDB-ID: 6zoj

SummaryFull reportAbout validation report
History
DepositionJul 7, 2020-
Header (metadata) releaseJul 22, 2020-
Map releaseJul 22, 2020-
UpdateOct 21, 2020-
Current statusOct 21, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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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
  • Imaged by UCSF Chimera
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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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