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- PDB-6zoj: SARS-CoV-2-Nsp1-40S complex, composite map -

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Basic information

Entry
Database: PDB / ID: 6zoj
TitleSARS-CoV-2-Nsp1-40S complex, composite map
Components
  • (40S ribosomal protein ...) x 31
  • 18S ribosomal RNA
  • 60S ribosomal protein L41
  • Non-structural protein 1
  • Receptor of activated protein C kinase 1
  • Ribosomal protein S27aRibosome
KeywordsTRANSLATION / inhibitor / mRNA channel / 40S ribosomal subunit
Function / homology
Function and homology information


positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / mammalian oogenesis stage / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation / positive regulation of Golgi to plasma membrane protein transport / response to extracellular stimulus / negative regulation of RNA splicing / IRE1-RACK1-PP2A complex / ubiquitin ligase inhibitor activity ...positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / mammalian oogenesis stage / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation / positive regulation of Golgi to plasma membrane protein transport / response to extracellular stimulus / negative regulation of RNA splicing / IRE1-RACK1-PP2A complex / ubiquitin ligase inhibitor activity / laminin receptor activity / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of cell division / activation-induced cell death of T cells / negative regulation of endoplasmic reticulum unfolded protein response / negative regulation of hydrogen peroxide-induced neuron death / positive regulation of DNA N-glycosylase activity / negative regulation of DNA repair / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of ubiquitin protein ligase activity / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of ceramide biosynthetic process / erythrocyte homeostasis / NF-kappaB complex / negative regulation of phagocytosis / regulation of establishment of cell polarity / positive regulation of endodeoxyribonuclease activity / signaling adaptor activity / oxidized purine DNA binding / negative regulation of Wnt signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process / protein kinase A binding / supercoiled DNA binding / positive regulation of mitochondrial depolarization / translation regulator activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / phagocytic cup / ion channel inhibitor activity / negative regulation of smoothened signaling pathway / positive regulation of apoptotic signaling pathway / erythrocyte development / ubiquitin-like protein conjugating enzyme binding / iron-sulfur cluster binding / TOR signaling / positive regulation of cellular component movement / fibroblast growth factor binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / rescue of stalled ribosome / positive regulation of T cell receptor signaling pathway / poly(U) RNA binding / stress granule assembly / monocyte chemotaxis / DNA-(apurinic or apyrimidinic site) lyase / 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 / 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of activated T cell proliferation / GABA-ergic synapse / positive regulation of cyclic-nucleotide phosphodiesterase activity / ribosomal small subunit export from nucleus / regulation of tumor necrosis factor-mediated signaling pathway / maturation of SSU-rRNA / regulation of translational fidelity / gastrulation / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein kinase B signaling / spindle assembly / negative regulation of ubiquitin-dependent protein catabolic process / small-subunit processome / positive regulation of JUN kinase activity / SRP-dependent cotranslational protein targeting to membrane / ribosomal small subunit biogenesis / translation initiation factor binding / positive regulation of DNA repair / molecular adaptor activity / polysome / positive regulation of microtubule polymerization / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / laminin binding / positive regulation of cell cycle / endoplasmic reticulum mannose trimming / Hsp70 protein binding / negative regulation of peptidyl-serine phosphorylation / cytoplasmic pattern recognition receptor signaling pathway / tubulin binding / erythrocyte differentiation / innate immune response in mucosa / positive regulation of intrinsic apoptotic signaling pathway / polysomal ribosome / SH2 domain binding / MyD88-independent toll-like receptor signaling pathway / translational initiation / mRNA 3'-UTR binding / negative regulation of protein ubiquitination
Ribosomal protein L41 / Ribosomal protein S3, conserved site / Non-structural protein NSP1, betacoronavirus / Ribosomal protein S19 conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ribosomal protein S17, conserved site / Ubiquitin domain ...Ribosomal protein L41 / Ribosomal protein S3, conserved site / Non-structural protein NSP1, betacoronavirus / Ribosomal protein S19 conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ribosomal protein S17, conserved site / Ubiquitin domain / Ubiquitin conserved site / 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 S21e, conserved site / DPUP/SUD, C-terminal, betacoronavirus / Ribosomal protein S19e, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein 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 / Ribosomal protein S4, conserved site / WD40-repeat-containing domain / K homology domain-like, alpha/beta / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / Non-structural protein NSP7, coronavirus / 50S ribosomal protein L30e-like / Non-structural protein NSP9 superfamily, coronavirus / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S17e-like superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / RNA synthesis protein NSP10 superfamily, coronavirus / WD40-repeat-containing domain superfamily / Ribosomal protein S8 superfamily / Non-structural protein NSP3, nucleic acid-binding (NAR) domain, betacoronavirus / Non-structural protein NSP4, C-terminal, coronavirus / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein S4, C-terminal domain / Ubiquitin-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase / Ribosomal protein S15P / Ribosomal protein S4e, central region / Ribosomal protein S19/S15, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / Non-structural protein NSP3, N-terminal, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / (+) RNA virus helicase core domain / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S28e conserved site / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein S2, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / 40S ribosomal protein SA / Ribosomal protein S17, archaeal/eukaryotic / Non-structural protein NSP8, coronavirus-like / Non-structural protein NSP9, coronavirus / Ribosomal protein S10 domain superfamily / Ribosomal protein S12/S23 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / K Homology domain, type 2 / 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 / KOW / Ribosomal protein S30 / Ribosomal protein S27a / Ribosomal protein S13-like, H2TH / 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 / RNA polymerase, N-terminal, coronaviral / Ribosomal protein L41 / Non-structural protein 14, coronavirus / Non-structural protein NSP16, coronavirus-like / S15/NS1, RNA-binding / K homology domain superfamily, prokaryotic type
40S ribosomal protein S18 / 40S ribosomal protein S15 / 40S ribosomal protein S6 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S11 / 40S ribosomal protein S13 / 40S ribosomal protein S29 / 40S ribosomal protein S28 / 40S ribosomal protein S17 / 40S ribosomal protein S14 ...40S ribosomal protein S18 / 40S ribosomal protein S15 / 40S ribosomal protein S6 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S11 / 40S ribosomal protein S13 / 40S ribosomal protein S29 / 40S ribosomal protein S28 / 40S ribosomal protein S17 / 40S ribosomal protein S14 / 40S ribosomal protein S16 / 40S ribosomal protein S15a / 40S ribosomal protein S8 / 40S ribosomal protein S7 / 40S ribosomal protein S3a / 40S ribosomal protein S20 / 40S ribosomal protein S23 / 40S ribosomal protein SA / 40S ribosomal protein S30 / 40S ribosomal protein S10 / 60S ribosomal protein L41 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S21 / Receptor of activated protein C kinase 1 / 40S ribosomal protein S27a / gb:151415227: / 40S ribosomal protein S26 / 40S ribosomal protein S25 / Replicase polyprotein 1ab / 40S ribosomal protein S24 / 40S ribosomal protein S9 / 40S ribosomal protein S27 / 40S ribosomal protein S19 / 40S ribosomal protein S12 / 40S ribosomal protein S3 / 40S ribosomal protein S2 / 40S ribosomal protein S5
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSchubert, K. / Karousis, E.D. / Jomaa, A. / Scaiola, A. / Echeverria, B. / Gurzeler, L.-A. / Leibundgut, M.L. / Thiel, V. / Muehlemann, O. / Ban, N.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation173085 Switzerland
Swiss National Science Foundation182341 Switzerland
Swiss National Science Foundation182831 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 Report
SummaryFull reportAbout validation report
History
DepositionJul 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
2: 18S ribosomal RNA
A: 40S ribosomal protein SA
B: 40S ribosomal protein S3a
C: 40S ribosomal protein S2
D: 40S ribosomal protein S3
E: 40S ribosomal protein S4, X isoform
F: 40S ribosomal protein S5
G: 40S ribosomal protein S6
H: 40S ribosomal protein S7
I: 40S ribosomal protein S8
J: 40S ribosomal protein S9
K: 40S ribosomal protein S10
L: 40S ribosomal protein S11
M: 40S ribosomal protein S12
N: 40S ribosomal protein S13
O: 40S ribosomal protein S14
P: 40S ribosomal protein S15
Q: 40S ribosomal protein S16
R: 40S ribosomal protein S17
S: 40S ribosomal protein S18
T: 40S ribosomal protein S19
U: 40S ribosomal protein S20
V: 40S ribosomal protein S21
W: 40S ribosomal protein S15a
X: 40S ribosomal protein S23
Y: 40S ribosomal protein S24
Z: 40S ribosomal protein S25
a: 40S ribosomal protein S26
b: 40S ribosomal protein S27
c: 40S ribosomal protein S28
d: 40S ribosomal protein S29
e: 40S ribosomal protein S30
f: Ribosomal protein S27a
g: Receptor of activated protein C kinase 1
j: Non-structural protein 1
h: 60S ribosomal protein L41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,236,182205
Polymers1,231,95136
Non-polymers4,231169
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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40S ribosomal protein ... , 31 types, 31 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcde

#2: Protein 40S ribosomal protein SA / / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2


Mass: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#3: Protein 40S ribosomal protein S3a / / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#4: Protein 40S ribosomal protein S2 / / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#5: Protein 40S ribosomal protein S3 / / Small ribosomal subunit protein uS3


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#6: Protein 40S ribosomal protein S4, X isoform / Ribosome / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#7: Protein 40S ribosomal protein S5 / / Small ribosomal subunit protein uS7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#8: Protein 40S ribosomal protein S6 / / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#9: Protein 40S ribosomal protein S7 / / Small ribosomal subunit protein eS7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#10: Protein 40S ribosomal protein S8 / / Small ribosomal subunit protein eS8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#11: Protein 40S ribosomal protein S9 / / Small ribosomal subunit protein uS4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#12: Protein 40S ribosomal protein S10 / / Small ribosomal subunit protein eS10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#13: Protein 40S ribosomal protein S11 / / Small ribosomal subunit protein uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#14: Protein 40S ribosomal protein S12 / / Small ribosomal subunit protein eS12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398
#15: Protein 40S ribosomal protein S13 / / Small ribosomal subunit protein uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277
#16: Protein 40S ribosomal protein S14 / / Small ribosomal subunit protein uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263
#17: Protein 40S ribosomal protein S15 / / RIG protein / Small ribosomal subunit protein uS19


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62841
#18: Protein 40S ribosomal protein S16 / / Small ribosomal subunit protein uS9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62249
#19: Protein 40S ribosomal protein S17 / / Small ribosomal subunit protein eS17


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#20: Protein 40S ribosomal protein S18 / / Ke-3 / Ke3 / Small ribosomal subunit protein uS13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62269
#21: Protein 40S ribosomal protein S19 / / Small ribosomal subunit protein eS19


Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#22: Protein 40S ribosomal protein S20 / / Small ribosomal subunit protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60866
#23: Protein 40S ribosomal protein S21 / / Small ribosomal subunit protein eS21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#24: Protein 40S ribosomal protein S15a / / Small ribosomal subunit protein uS8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#25: Protein 40S ribosomal protein S23 / / Small ribosomal subunit protein uS12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62266
#26: Protein 40S ribosomal protein S24 / / Small ribosomal subunit protein eS24


Mass: 15107.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#27: Protein 40S ribosomal protein S25 / / Small ribosomal subunit protein eS25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62851
#28: Protein 40S ribosomal protein S26 / / Small ribosomal subunit protein eS26


Mass: 11645.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#29: Protein 40S ribosomal protein S27 / / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27


Mass: 9210.843 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#30: Protein 40S ribosomal protein S28 / / Small ribosomal subunit protein eS28


Mass: 6878.940 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#31: Protein 40S ribosomal protein S29 / / Small ribosomal subunit protein uS14


Mass: 6559.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273
#32: Protein 40S ribosomal protein S30 / / Small ribosomal subunit protein eS30


Mass: 6302.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861

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Protein , 3 types, 3 molecules fgj

#33: Protein Ribosomal protein S27a / Ribosome


Mass: 8453.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5RKT7, UniProt: P62979*PLUS
#34: Protein Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1


Mass: 34857.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244
#35: Protein Non-structural protein 1 / pp1ab / ORF1ab polyprotein / Non-structural protein 1


Mass: 19801.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase, RNA-directed RNA polymerase, DNA ...References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase, RNA-directed RNA polymerase, DNA helicase, RNA helicase, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds, Transferases; Transferring one-carbon groups; Methyltransferases

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RNA chain / Protein/peptide , 2 types, 2 molecules 2h

#1: RNA chain 18S ribosomal RNA /


Mass: 602777.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 151415227
#36: Protein/peptide 60S ribosomal protein L41 / / HG12 / Large ribosomal subunit protein eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62945

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Non-polymers , 2 types, 169 molecules

#37: Chemical...
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 166 / Source method: obtained synthetically / Formula: Mg
#38: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1SARS-CoV-2-Nsp1-40S complex, composite mapCOMPLEX#1-#360MULTIPLE SOURCES
2Ribosomal proteinsRibosomal proteinCOMPLEX#1-#34, #361NATURAL
3SARS-CoV-2-Nsp1COMPLEX#351RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Severe acute respiratory syndrome coronavirus 22697049
Source (recombinant)Organism: Escherichia coli K-12 (bacteria)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118765 / Symmetry type: POINT
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00280581
ELECTRON MICROSCOPYf_angle_d0.485116927
ELECTRON MICROSCOPYf_dihedral_angle_d15.31236066
ELECTRON MICROSCOPYf_chiral_restr0.03414443
ELECTRON MICROSCOPYf_plane_restr0.0038511

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