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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
Sample
  • Complex: SARS-CoV-2-Nsp1-40S, focused on body
    • Complex: Ribosomal proteins
      • RNA: x 1 types
      • Protein or peptide: x 20 types
    • Complex: SARS-CoV-2-Nsp1-40S
      • Protein or peptide: x 1 types
  • Ligand: x 2 types
Function / homology
Function and homology information


negative regulation of RNA splicing / neural crest cell differentiation / positive regulation of ubiquitin-protein transferase activity / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition ...negative regulation of RNA splicing / neural crest cell differentiation / positive regulation of ubiquitin-protein transferase activity / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / mammalian oogenesis stage / fibroblast growth factor binding / activation-induced cell death of T cells / Protein hydroxylation / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response / positive regulation of cell cycle / Major pathway of rRNA processing in the nucleolus and cytosol / erythrocyte development / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Protein methylation / Nuclear events stimulated by ALK signaling in cancer / translation regulator activity / laminin binding / stress granule assembly / Mitotic Prometaphase / rough endoplasmic reticulum / 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) / antiviral innate immune response / EML4 and NUDC in mitotic spindle formation / gastrulation / translation initiation factor binding / Resolution of Sister Chromatid Cohesion / cytosolic ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / erythrocyte differentiation / maturation of SSU-rRNA / innate immune response in mucosa / positive regulation of translation / neural tube closure / small-subunit processome / mRNA 3'-UTR binding / translational initiation / RHO GTPases Activate Formins / maintenance of translational fidelity / response to virus / placenta development / mRNA 5'-UTR binding / RMTs methylate histone arginines / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / G1/S transition of mitotic cell cycle / Separation of Sister Chromatids / rRNA processing / ribosomal small subunit biogenesis / antimicrobial humoral immune response mediated by antimicrobial peptide / small ribosomal subunit rRNA binding / protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / antibacterial humoral response / 5'-3' RNA helicase activity / ribosome binding / Lyases; Phosphorus-oxygen lyases / glucose homeostasis / ribosomal small subunit assembly / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / virus receptor activity / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / TRAF3-dependent IRF activation pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / small ribosomal subunit / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / T cell differentiation in thymus
Similarity search - Function
40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S21e, conserved site ...40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S30 / : / Ribosomal protein S30 / Ribosomal protein S7e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / : / Ribosomal protein S6, eukaryotic / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein S2 signature 2. / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ribosomal protein S2 signature 1. / RNA-dependent RNA polymerase, SARS-CoV-like / : / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Nonstructural protein 14, betacoronavirus / Ribosomal protein S5 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / NSP15, NendoU domain, coronavirus / Ribosomal protein S5, C-terminal domain
Similarity search - Domain/homology
Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Replicase polyprotein 1ab / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 ...Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Replicase polyprotein 1ab / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4, X isoform / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS26 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS32 / Small ribosomal subunit protein eS21
Similarity search - Component
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.
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
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.8
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  • Surface view with fitted model
  • Atomic models: PDB-6zok
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zok
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11321.png

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

Histogram

Histogram (log scale)
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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Mask #1

Fileemd_11321_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11321_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_11321_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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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
Components
  • Complex: SARS-CoV-2-Nsp1-40S, focused on body
    • Complex: Ribosomal proteins
      • RNA: 18S ribosomal RNA
      • Protein or peptide: 40S ribosomal protein SA
      • Protein or peptide: 40S ribosomal protein S3a
      • Protein or peptide: 40S ribosomal protein S2
      • Protein or peptide: 40S ribosomal protein S4, X isoform
      • Protein or peptide: 40S ribosomal protein S6
      • Protein or peptide: 40S ribosomal protein S7
      • Protein or peptide: 40S ribosomal protein S8
      • Protein or peptide: 40S ribosomal protein S9
      • Protein or peptide: 40S ribosomal protein S11
      • Protein or peptide: 40S ribosomal protein S13
      • Protein or peptide: 40S ribosomal protein S14
      • Protein or peptide: 40S ribosomal protein S17
      • Protein or peptide: 40S ribosomal protein S21
      • Protein or peptide: 40S ribosomal protein S15a
      • Protein or peptide: 40S ribosomal protein S23
      • Protein or peptide: 40S ribosomal protein S24
      • Protein or peptide: 40S ribosomal protein S26
      • Protein or peptide: 40S ribosomal protein S27
      • Protein or peptide: 40S ribosomal protein S30
      • Protein or peptide: 60S ribosomal protein L41
    • Complex: SARS-CoV-2-Nsp1-40S
      • Protein or peptide: Non-structural protein 1
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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

SupramoleculeName: SARS-CoV-2-Nsp1-40S, focused on body / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#22

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Supramolecule #2: Ribosomal proteins

SupramoleculeName: Ribosomal proteins / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#20, #22
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: SARS-CoV-2-Nsp1-40S

SupramoleculeName: SARS-CoV-2-Nsp1-40S / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #21
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: 18S ribosomal RNA

MacromoleculeName: 18S ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 602.777875 KDa
SequenceString: UACCUGGUUG AUCCUGCCAG UAGCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUGGUUCCU UUGGUCGCUC GCUCCUCUCC UACUUGGAUA ACUGUGGUAA U UCUAGAGC ...String:
UACCUGGUUG AUCCUGCCAG UAGCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUGGUUCCU UUGGUCGCUC GCUCCUCUCC UACUUGGAUA ACUGUGGUAA U UCUAGAGC UAAUACAUGC CGACGGGCGC UGACCCCCUU CGCGGGGGGG AUGCGUGCAU UUAUCAGAUC AAAACCAACC CG GUCAGCC CCUCUCCGGC CCCGGCCGGG GGGCGGGCGC CGGCGGCUUU GGUGACUCUA GAUAACCUCG GGCCGAUCGC ACG CCCCCC GUGGCGGCGA CGACCCAUUC GAACGUCUGC CCUAUCAACU UUCGAUGGUA GUCGCCGUGC CUACCAUGGU GACC ACGGG UGACGGGGAA UCAGGGUUCG AUUCCGGAGA GGGAGCCUGA GAAACGGCUA CCACAUCCAA GGAAGGCAGC AGGCG CGCA AAUUACCCAC UCCCGACCCG GGGAGGUAGU GACGAAAAAU AACAAUACAG GACUCUUUCG AGGCCCUGUA AUUGGA AUG AGUCCACUUU AAAUCCUUUA ACGAGGAUCC AUUGGAGGGC AAGUCUGGUG CCAGCAGCCG CGGUAAUUCC AGCUCCA AU AGCGUAUAUU AAAGUUGCUG CAGUUAAAAA GCUCGUAGUU GGAUCUUGGG AGCGGGCGGG CGGUCCGCCG CGAGGCGA G CCACCGCCCG UCCCCGCCCC UUGCCUCUCG GCGCCCCCUC GAUGCUCUUA GCUGAGUGUC CCGCGGGGCC CGAAGCGUU UACUUUGAAA AAAUUAGAGU GUUCAAAGCA GGCCCGAGCC GCCUGGAUAC CGCAGCUAGG AAUAAUGGAA UAGGACCGCG GUUCUAUUU UGUUGGUUUU CGGAACUGAG GCCAUGAUUA AGAGGGACGG CCGGGGGCAU UCGUAUUGCG CCGCUAGAGG U GAAAUUCU UGGACCGGCG CAAGACGGAC CAGAGCGAAA GCAUUUGCCA AGAAUGUUUU CAUUAAUCAA GAACGAAAGU CG GAGGUUC GAAGACGAUC AGAUACCGUC GUAGUUCCGA CCAUAAACGA UGCCGACCGG CGAUGCGGCG GCGUUAUUCC CAU GACCCG CCGGGCAGCU UCCGGGAAAC CAAAGUCUUU GGGUUCCGGG GGGAGUAUGG UUGCAAAGCU GAAACUUAAA GGAA UUGAC GGAAGGGCAC CACCAGGAGU GGAGCCUGCG GCUUAAUUUG ACUCAACACG GGAAACCUCA CCCGGCCCGG ACACG GACA GGAUUGACAG AUUGAUAGCU CUUUCUCGAU UCCGUGGGUG GUGGUGCAUG GCCGUUCUUA GUUGGUGGAG CGAUUU GUC UGGUUAAUUC CGAUAACGAA CGAGACUCUG GCAUGCUAAC UAGUUACGCG ACCCCCGAGC GGUCGGCGUC CCCCAAC UU CUUAGAGGGA CAAGUGGCGU UCAGCCACCC GAGAUUGAGC AAUAACAGGU CUGUGAUGCC CUUAGAUGUC CGGGGCUG C ACGCGCGCUA CACUGACUGG CUCAGCGUGU GCCUACCCUA CGCCGGCAGG CGCGGGUAAC CCGUUGAACC CCAUUCGUG AUGGGGAUCG GGGAUUGCAA UUAUUCCCCA UGAACGAGGA AUUCCCAGUA AGUGCGGGUC AUAAGCUUGC GUUGAUUAAG UCCCUGCCC UUUGUACACA CCGCCCGUCG CUACUACCGA UUGGAUGGUU UAGUGAGGCC CUCGGAUCGG CCCCGCCGGG G UCGGCCCA CGGCCCUGGC GGAGCGCUGA GAAGACGGUC GAACUUGACU AUCUAGAGGA AGUAAAAGUC GUAACAAGGU UU CCGUAGG UGAACCUGCG GAAGGAUCAU UA

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Macromolecule #2: 40S ribosomal protein SA

MacromoleculeName: 40S ribosomal protein SA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 32.883938 KDa
SequenceString: MSGALDVLQM KEEDVLKFLA AGTHLGGTNL DFQMEQYIYK RKSDGIYIIN LKRTWEKLLL AARAIVAIEN PADVSVISSR NTGQRAVLK FAAATGATPI AGRFTPGTFT NQIQAAFREP RLLVVTDPRA DHQPLTEASY VNLPTIALCN TDSPLRYVDI A IPCNNKGA ...String:
MSGALDVLQM KEEDVLKFLA AGTHLGGTNL DFQMEQYIYK RKSDGIYIIN LKRTWEKLLL AARAIVAIEN PADVSVISSR NTGQRAVLK FAAATGATPI AGRFTPGTFT NQIQAAFREP RLLVVTDPRA DHQPLTEASY VNLPTIALCN TDSPLRYVDI A IPCNNKGA HSVGLMWWML AREVLRMRGT ISREHPWEVM PDLYFYRDPE EIEKEEQAAA EKAVTKEEFQ GEWTAPAPEF TA TQPEVAD WSEGVQVPSV PIQQFPTEDW SAQPATEDWS AAPTAQATEW VGATTDWS

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Macromolecule #3: 40S ribosomal protein S3a

MacromoleculeName: 40S ribosomal protein S3a / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 30.002061 KDa
SequenceString: MAVGKNKRLT KGGKKGAKKK VVDPFSKKDW YDVKAPAMFN IRNIGKTLVT RTQGTKIASD GLKGRVFEVS LADLQNDEVA FRKFKLITE DVQGKNCLTN FHGMDLTRDK MCSMVKKWQT MIEAHVDVKT TDGYLLRLFC VGFTKKRNNQ IRKTSYAQHQ Q VRQIRKKM ...String:
MAVGKNKRLT KGGKKGAKKK VVDPFSKKDW YDVKAPAMFN IRNIGKTLVT RTQGTKIASD GLKGRVFEVS LADLQNDEVA FRKFKLITE DVQGKNCLTN FHGMDLTRDK MCSMVKKWQT MIEAHVDVKT TDGYLLRLFC VGFTKKRNNQ IRKTSYAQHQ Q VRQIRKKM MEIMTREVQT NDLKEVVNKL IPDSIGKDIE KACQSIYPLH DVFVRKVKML KKPKFELGKL MELHGEGSSS GK ATGDETG AKVERADGYE PPVQESV

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Macromolecule #4: 40S ribosomal protein S2

MacromoleculeName: 40S ribosomal protein S2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 31.376516 KDa
SequenceString: MADDAGAAGG PGGPGGPGMG NRGGFRGGFG SGIRGRGRGR GRGRGRGRGA RGGKAEDKEW MPVTKLGRLV KDMKIKSLEE IYLFSLPIK ESEIIDFFLG ASLKDEVLKI MPVQKQTRAG QRTRFKAFVA IGDYNGHVGL GVKCSKEVAT AIRGAIILAK L SIVPVRRG ...String:
MADDAGAAGG PGGPGGPGMG NRGGFRGGFG SGIRGRGRGR GRGRGRGRGA RGGKAEDKEW MPVTKLGRLV KDMKIKSLEE IYLFSLPIK ESEIIDFFLG ASLKDEVLKI MPVQKQTRAG QRTRFKAFVA IGDYNGHVGL GVKCSKEVAT AIRGAIILAK L SIVPVRRG YWGNKIGKPH TVPCKVTGRC GSVLVRLIPA PRGTGIVSAP VPKKLLMMAG IDDCYTSARG CTATLGNFAK AT FDAISKT YSYLTPDLWK ETVFTKSPYQ EFTDHLVKTH TRVSVQRTQA PAVATT

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Macromolecule #5: 40S ribosomal protein S4, X isoform

MacromoleculeName: 40S ribosomal protein S4, X isoform / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 29.654869 KDa
SequenceString: MARGPKKHLK RVAAPKHWML DKLTGVFAPR PSTGPHKLRE CLPLIIFLRN RLKYALTGDE VKKICMQRFI KIDGKVRTDI TYPAGFMDV ISIDKTGENF RLIYDTKGRF AVHRITPEEA KYKLCKVRKI FVGTKGIPHL VTHDARTIRY PDPLIKVNDT I QIDLETGK ...String:
MARGPKKHLK RVAAPKHWML DKLTGVFAPR PSTGPHKLRE CLPLIIFLRN RLKYALTGDE VKKICMQRFI KIDGKVRTDI TYPAGFMDV ISIDKTGENF RLIYDTKGRF AVHRITPEEA KYKLCKVRKI FVGTKGIPHL VTHDARTIRY PDPLIKVNDT I QIDLETGK ITDFIKFDTG NLCMVTGGAN LGRIGVITNR ERHPGSFDVV HVKDANGNSF ATRLSNIFVI GKGNKPWISL PR GKGIRLT IAEERDKRLA AKQSSG

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Macromolecule #6: 40S ribosomal protein S6

MacromoleculeName: 40S ribosomal protein S6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 28.751906 KDa
SequenceString: MKLNISFPAT GCQKLIEVDD ERKLRTFYEK RMATEVAADA LGEEWKGYVV RISGGNDKQG FPMKQGVLTH GRVRLLLSKG HSCYRPRRT GERKRKSVRG CIVDANLSVL NLVIVKKGEK DIPGLTDTTV PRRLGPKRAS RIRKLFNLSK EDDVRQYVVR K PLNKEGKK ...String:
MKLNISFPAT GCQKLIEVDD ERKLRTFYEK RMATEVAADA LGEEWKGYVV RISGGNDKQG FPMKQGVLTH GRVRLLLSKG HSCYRPRRT GERKRKSVRG CIVDANLSVL NLVIVKKGEK DIPGLTDTTV PRRLGPKRAS RIRKLFNLSK EDDVRQYVVR K PLNKEGKK PRTKAPKIQR LVTPRVLQHK RRRIALKKQR TKKNKEEAAE YAKLLAKRMK EAKEKRQEQI AKRRRLSSLR AS TSKSESS QK

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Macromolecule #7: 40S ribosomal protein S7

MacromoleculeName: 40S ribosomal protein S7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 22.168914 KDa
SequenceString: MFSSSAKIVK PNGEKPDEFE SGISQALLEL EMNSDLKAQL RELNITAAKE IEVGGGRKAI IIFVPVPQLK SFQKIQVRLV RELEKKFSG KHVVFIAQRR ILPKPTRKSR TKNKQKRPRS RTLTAVHDAI LEDLVFPSEI VGKRIRVKLD GSRLIKVHLD K AQQNNVEH ...String:
MFSSSAKIVK PNGEKPDEFE SGISQALLEL EMNSDLKAQL RELNITAAKE IEVGGGRKAI IIFVPVPQLK SFQKIQVRLV RELEKKFSG KHVVFIAQRR ILPKPTRKSR TKNKQKRPRS RTLTAVHDAI LEDLVFPSEI VGKRIRVKLD GSRLIKVHLD K AQQNNVEH KVETFSGVYK KLTGKDVNFE FPEFQL

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Macromolecule #8: 40S ribosomal protein S8

MacromoleculeName: 40S ribosomal protein S8 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 24.263387 KDa
SequenceString: MGISRDNWHK RRKTGGKRKP YHKKRKYELG RPAANTKIGP RRIHTVRVRG GNKKYRALRL DVGNFSWGSE CCTRKTRIID VVYNASNNE LVRTKTLVKN CIVLIDSTPY RQWYESHYAL PLGRKKGAKL TPEEEEILNK KRSKKIQKKY DERKKNAKIS S LLEEQFQQ ...String:
MGISRDNWHK RRKTGGKRKP YHKKRKYELG RPAANTKIGP RRIHTVRVRG GNKKYRALRL DVGNFSWGSE CCTRKTRIID VVYNASNNE LVRTKTLVKN CIVLIDSTPY RQWYESHYAL PLGRKKGAKL TPEEEEILNK KRSKKIQKKY DERKKNAKIS S LLEEQFQQ GKLLACIASR PGQCGRADGY VLEGKELEFY LRKIKARKGK

+
Macromolecule #9: 40S ribosomal protein S9

MacromoleculeName: 40S ribosomal protein S9 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 22.641564 KDa
SequenceString: MPVARSWVCR KTYVTPRRPF EKSRLDQELK LIGEYGLRNK REVWRVKFTL AKIRKAAREL LTLDEKDPRR LFEGNALLRR LVRIGVLDE GKMKLDYILG LKIEDFLERR LQTQVFKLGL AKSIHHARVL IRQRHIRVRK QVVNIPSFIV RLDSQKHIDF S LRSPYGGG ...String:
MPVARSWVCR KTYVTPRRPF EKSRLDQELK LIGEYGLRNK REVWRVKFTL AKIRKAAREL LTLDEKDPRR LFEGNALLRR LVRIGVLDE GKMKLDYILG LKIEDFLERR LQTQVFKLGL AKSIHHARVL IRQRHIRVRK QVVNIPSFIV RLDSQKHIDF S LRSPYGGG RPGRVKRKNA KKGQGGAGAG DDEEED

+
Macromolecule #10: 40S ribosomal protein S11

MacromoleculeName: 40S ribosomal protein S11 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 18.468826 KDa
SequenceString:
MADIQTERAY QKQPTIFQNK KRVLLGETGK EKLPRYYKNI GLGFKTPKEA IEGTYIDKKC PFTGNVSIRG RILSGVVTKM KMQRTIVIR RDYLHYIRKY NRFEKRHKNM SVHLSPCFRD VQIGDIVTVG ECRPLSKTVR FNVLKVTKAA GTKKQFQKF

+
Macromolecule #11: 40S ribosomal protein S13

MacromoleculeName: 40S ribosomal protein S13 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 17.259389 KDa
SequenceString:
MGRMHAPGKG LSQSALPYRR SVPTWLKLTS DDVKEQIYKL AKKGLTPSQI GVILRDSHGV AQVRFVTGNK ILRILKSKGL APDLPEDLY HLIKKAVAVR KHLERNRKDK DAKFRLILIE SRIHRLARYY KTKRVLPPNW KYESSTASAL VA

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Macromolecule #12: 40S ribosomal protein S14

MacromoleculeName: 40S ribosomal protein S14 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 16.302772 KDa
SequenceString:
MAPRKGKEKK EEQVISLGPQ VAEGENVFGV CHIFASFNDT FVHVTDLSGK ETICRVTGGM KVKADRDESS PYAAMLAAQD VAQRCKELG ITALHIKLRA TGGNRTKTPG PGAQSALRAL ARSGMKIGRI EDVTPIPSDS TRRKGGRRGR RL

+
Macromolecule #13: 40S ribosomal protein S17

MacromoleculeName: 40S ribosomal protein S17 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 15.578156 KDa
SequenceString:
MGRVRTKTVK KAARVIIEKY YTRLGNDFHT NKRVCEEIAI IPSKKLRNKI AGYVTHLMKR IQRGPVRGIS IKLQEEERER RDNYVPEVS ALDQEIIEVD PDTKEMLKLL DFGSLSNLQV TQPTVGMNFK TPRGPV

+
Macromolecule #14: 40S ribosomal protein S21

MacromoleculeName: 40S ribosomal protein S21 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 9.124389 KDa
SequenceString:
MQNDAGEFVD LYVPRKCSAS NRIIGAKDHA SIQMNVAEVD KVTGRFNGQF KTYAICGAIR RMGESDDSIL RLAKADGIVS KNF

+
Macromolecule #15: 40S ribosomal protein S15a

MacromoleculeName: 40S ribosomal protein S15a / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 14.865555 KDa
SequenceString:
MVRMNVLADA LKSINNAEKR GKRQVLIRPC SKVIVRFLTV MMKHGYIGEF EIIDDHRAGK IVVNLTGRLN KCGVISPRFD VQLKDLEKW QNNLLPSRQF GFIVLTTSAG IMDHEEARRK HTGGKILGFF F

+
Macromolecule #16: 40S ribosomal protein S23

MacromoleculeName: 40S ribosomal protein S23 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 15.844666 KDa
SequenceString:
MGKCRGLRTA RKLRSHRRDQ KWHDKQYKKA HLGTALKANP FGGASHAKGI VLEKVGVEAK QPNSAIRKCV RVQLIKNGKK ITAFVPNDG CLNFIEENDE VLVAGFGRKG HAVGDIPGVR FKVVKVANVS LLALYKGKKE RPRS

+
Macromolecule #17: 40S ribosomal protein S24

MacromoleculeName: 40S ribosomal protein S24 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 15.107924 KDa
SequenceString:
MNDTVTIRTR KFMTNRLLQR KQMVIDVLHP GKATVPKTEI REKLAKMYKT TPDVIFVFGF RTHFGGGKTT GFGMIYDSLD YAKKNEPKH RLARHGLYEK KKTSRKQRKE RKNRMKKVRG TAKANVGAGK K

+
Macromolecule #18: 40S ribosomal protein S26

MacromoleculeName: 40S ribosomal protein S26 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 11.645794 KDa
SequenceString:
TKKRRNNGRA KKGRGHVQPI RCTNCARCVP KDKAIKKFVI RNIVEAAAVR DISEASVFDA YVLPKLYVKL HYCVSCAIHS KVVRNRSRE ARKDRTPPPR FR

+
Macromolecule #19: 40S ribosomal protein S27

MacromoleculeName: 40S ribosomal protein S27 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 9.210843 KDa
SequenceString:
PLAKDLLHPS PEEEKRKHKK KRLVQSPNSY FMDVKCPGCY KITTVFSHAQ TVVLCVGCST VLCQPTGGKA RLTEGCSFRR KQ

+
Macromolecule #20: 40S ribosomal protein S30

MacromoleculeName: 40S ribosomal protein S30 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 6.30248 KDa
SequenceString:
GSLARAGKVR GQTPKVAKQE KKKKKTGRAK RRMQYNRRFV NVVPTFGKKK GPNANS

+
Macromolecule #21: Non-structural protein 1

MacromoleculeName: Non-structural protein 1 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 19.801287 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MESLVPGFNE KTHVQLSLPV LQVRDVLVRG FGDSVEEVLS EARQHLKDGT CGLVEVEKGV LPQLEQPYVF IKRSDARTAP HGHVMVELV AELEGIQYGR SGETLGVLVP HVGEIPVAYR KVLLRKNGNK GAGGHSYGAD LKSFDLGDEL GTDPYEDFQE N WNTKHSSG VTRELMRELN GG

+
Macromolecule #22: 60S ribosomal protein L41

MacromoleculeName: 60S ribosomal protein L41 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 3.473451 KDa
SequenceString:
MRAKWRKKRM RRLKRKRRKM RQRSK

+
Macromolecule #23: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 23 / Number of copies: 109 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #24: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 24 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5oa3

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 118765
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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