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- PDB-7k5i: SARS-COV-2 nsp1 in complex with human 40S ribosome -

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Basic information

Entry
Database: PDB / ID: 7k5i
TitleSARS-COV-2 nsp1 in complex with human 40S ribosome
Components
  • (40S ribosomal protein ...) x 32
  • 40S ribosomal rRNA18S
  • 60S ribosomal protein L41
  • Receptor of activated protein C kinase 1
  • SARS-COV-2 Nsp1
KeywordsRIBOSOME/VIRAL PROTEIN / nsp1 / 40S / RIBOSOME-VIRAL PROTEIN complex
Function / homology
Function and homology information


negative regulation of DNA repair / oxidized pyrimidine DNA binding / positive regulation of base-excision repair / positive regulation of DNA N-glycosylase activity / response to TNF agonist / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage ...negative regulation of DNA repair / oxidized pyrimidine DNA binding / positive regulation of base-excision repair / positive regulation of DNA N-glycosylase activity / response to TNF agonist / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / positive regulation of Golgi to plasma membrane protein transport / NF-kappaB complex / response to extracellular stimulus / IRE1-RACK1-PP2A complex / negative regulation of RNA splicing / 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 / negative regulation of endoplasmic reticulum unfolded protein response / supercoiled DNA binding / negative regulation of hydrogen peroxide-induced neuron death / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / positive regulation of ceramide biosynthetic process / signaling adaptor activity / erythrocyte homeostasis / negative regulation of phagocytosis / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of Wnt signaling pathway / 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 / translation regulator activity / 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 / rescue of stalled ribosome / positive regulation of cellular component movement / iron-sulfur cluster binding / fibroblast growth factor binding / stress granule assembly / positive regulation of apoptotic signaling pathway / poly(U) RNA binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / DNA-(apurinic or apyrimidinic site) lyase / monocyte chemotaxis / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of ubiquitin-protein transferase activity / BH3 domain binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of cyclic-nucleotide phosphodiesterase activity / spindle assembly / positive regulation of JUN kinase activity / TOR signaling / negative regulation of protein kinase B signaling / positive regulation of interleukin-2 production / regulation of tumor necrosis factor-mediated signaling pathway / ribosomal small subunit export from nucleus / SRP-dependent cotranslational protein targeting to membrane / maturation of SSU-rRNA / negative regulation of ubiquitin-dependent protein catabolic process / regulation of translational fidelity / gastrulation / small-subunit processome / negative regulation of respiratory burst involved in inflammatory response / positive regulation of microtubule polymerization / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / polysome / viral transcription / translation initiation factor binding / ribosomal small subunit biogenesis / molecular adaptor activity / induction by virus of catabolism of host mRNA / positive regulation of DNA repair / Hsp70 protein binding / erythrocyte differentiation / suppression by virus of host ISG15 activity / laminin binding / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / positive regulation of cell cycle / exonuclease activity / suppression by virus of host NF-kappaB transcription factor activity / tubulin binding / omega peptidase activity / translational initiation / innate immune response in mucosa / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of protein ubiquitination / endodeoxyribonuclease activity / modulation by virus of host protein ubiquitination
Ribosomal protein S30 / G-protein beta WD-40 repeat / Ribosomal protein S19 conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S9 / Ribosomal protein S8 / Ribosomal protein S9, conserved site / Ubiquitin-like domain / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S27e ...Ribosomal protein S30 / G-protein beta WD-40 repeat / Ribosomal protein S19 conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S9 / Ribosomal protein S8 / Ribosomal protein S9, conserved site / Ubiquitin-like domain / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S27e / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S17, conserved site / Ribosomal protein S15 / Ubiquitin domain / Ribosomal protein S7e / Ribosomal protein S12e / Ribosomal protein S28e / Ribosomal protein S17/S11 / Ubiquitin conserved site / Non-structural protein NSP1, betacoronavirus / DPUP/SUD, C-terminal, betacoronavirus / WD40 repeat, conserved site / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein SA / Ribosomal protein S14 / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S8e / Ribosomal protein S2, eukaryotic / Ribosomal protein S10 domain / Ribosomal protein S4e, central region / Non-structural protein NSP3, single-stranded poly(A) binding domain, betacoronavirus / Ribosomal protein S4/S9 / Ribosomal protein S26e / Non-structural protein NSP3, N-terminal, betacoronavirus / Ribosomal protein S4e / Ribosomal protein S7 domain / Ribosomal protein S5 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S15P / Ribosomal protein S5/S7 / RNA synthesis protein NSP10, coronavirus / Ribosomal protein S19e / Nucleic acid-binding, OB-fold / Ribosomal S24e conserved site / Ribosomal protein S4, conserved site / WD40-repeat-containing domain / Zinc-binding ribosomal protein / K homology domain-like, alpha/beta / WD40/YVTN repeat-like-containing domain superfamily / Non-structural protein NSP8, coronavirus-like / Non-structural protein NSP7, coronavirus / Ribosomal protein S2, conserved site / Ribosomal protein S13/S15, N-terminal / Non-structural protein NSP9, coronavirus / Ribosomal protein L2, domain 2 / Ribosomal protein L23/L15e core domain superfamily / Peptidase C16, coronavirus / Ribosomal protein S5, N-terminal / Ribosomal protein S4e, N-terminal / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal S11, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S8e, conserved site / K homology domain superfamily, prokaryotic type / Peptidase C30, coronavirus / Ribosomal protein S6e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein L41 / Peptidase S1, PA clan / Ribosomal protein S21e, conserved site / Ribosomal protein S19e, conserved site / S15/NS1, RNA-binding / Ribosomal protein S4e, N-terminal, conserved site / Non-structural protein NSP16, coronavirus-like / Ribosomal protein S17e, conserved site / Non-structural protein NSP14, coronavirus / Ribosomal protein S14, conserved site / RNA polymerase, N-terminal, coronaviral / Ribosomal protein S13-like, H2TH / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S17e / 30s ribosomal protein S13, C-terminal / Ribosomal protein S28e conserved site / K Homology domain, type 2 / Ribosomal protein S25 / Ribosomal protein S14/S29 / Replicase polyprotein, nucleic acid-binding domain superfamily / Ribosomal protein S8e subdomain, eukaryotes / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Ribosomal protein S4, KOW domain / DNA2/NAM7 helicase-like, C-terminal / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / S27a-like superfamily / Non-structural protein NSP15, middle domain superfamily / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein S21e superfamily
40S ribosomal protein S23 / 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 S25 / 40S ribosomal protein S27a ...40S ribosomal protein S23 / 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 S25 / 40S ribosomal protein S27a / 40S ribosomal protein S26 / 40S ribosomal protein S28 / 40S ribosomal protein S30 / 60S ribosomal protein L41 / 40S ribosomal protein S21 / Receptor of activated protein C kinase 1 / 40S ribosomal protein S18 / 40S ribosomal protein SA / 40S ribosomal protein S14 / 40S ribosomal protein S27 / 40S ribosomal protein S17 / Replicase polyprotein 1ab / 40S ribosomal protein S2 / 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 / gb:337376:
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWang, L. / Shi, M. / Wu, H.
CitationJournal: bioRxiv : the preprint server for biology / Year: 2020
Title: SARS-CoV-2 Nsp1 suppresses host but not viral translation through a bipartite mechanism.
Abstract: The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a highly contagious virus that underlies the current COVID-19 pandemic. SARS-CoV-2 is thought to disable various features of host ...The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a highly contagious virus that underlies the current COVID-19 pandemic. SARS-CoV-2 is thought to disable various features of host immunity and cellular defense. The SARS-CoV-2 nonstructural protein 1 (Nsp1) is known to inhibit host protein translation and could be a target for antiviral therapy against COVID-19. However, how SARS-CoV-2 circumvents this translational blockage for the production of its own proteins is an open question. Here, we report a bipartite mechanism of SARS-CoV-2 Nsp1 which operates by: (1) hijacking the host ribosome via direct interaction of its C-terminal domain (CT) with the 40S ribosomal subunit and (2) specifically lifting this inhibition for SARS-CoV-2 via a direct interaction of its N-terminal domain (NT) with the 5' untranslated region (5' UTR) of SARS-CoV-2 mRNA. We show that while Nsp1-CT is sufficient for binding to 40S and inhibition of host protein translation, the 5' UTR of SARS-CoV-2 mRNA removes this inhibition by binding to Nsp1-NT, suggesting that the Nsp1-NT-UTR interaction is incompatible with the Nsp1-CT-40S interaction. Indeed, lengthening the linker between Nsp1-NT and Nsp1-CT of Nsp1 progressively reduced the ability of SARS-CoV-2 5' UTR to escape the translational inhibition, supporting that the incompatibility is likely steric in nature. The short SL1 region of the 5' UTR is required for viral mRNA translation in the presence of Nsp1. Thus, our data provide a comprehensive view on how Nsp1 switches infected cells from host mRNA translation to SARS-CoV-2 mRNA translation, and that Nsp1 and 5' UTR may be targeted for anti-COVID-19 therapeutics.
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
R: 40S ribosomal protein S17
2: 40S ribosomal rRNA18S
d: 40S ribosomal protein S29
D: 40S ribosomal protein S3
F: 40S ribosomal protein S5
K: 40S ribosomal protein S10
M: 40S ribosomal protein S12
P: 40S ribosomal protein S15
Q: 40S ribosomal protein S16
S: 40S ribosomal protein S18
T: 40S ribosomal protein S19
U: 40S ribosomal protein S20
Z: 40S ribosomal protein S25
c: 40S ribosomal protein S28
f: 40S ribosomal protein S27a
g: Receptor of activated protein C kinase 1
A: 40S ribosomal protein SA
B: 40S ribosomal protein S3a
C: 40S ribosomal protein S2
E: 40S ribosomal protein S4, X isoform
G: 40S ribosomal protein S6
H: 40S ribosomal protein S7
I: 40S ribosomal protein S8
J: 40S ribosomal protein S9
L: 40S ribosomal protein S11
N: 40S ribosomal protein S13
O: 40S ribosomal protein S14
V: 40S ribosomal protein S21
W: 40S ribosomal protein S15a
X: 40S ribosomal protein S23
Y: 40S ribosomal protein S24
a: 40S ribosomal protein S26
b: 40S ribosomal protein S27
e: 40S ribosomal protein S30
h: 60S ribosomal protein L41
1: SARS-COV-2 Nsp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,242,94440
Polymers1,242,72436
Non-polymers2214
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area184570 Å2
ΔGint-1365 kcal/mol
Surface area402780 Å2

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Components

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40S ribosomal protein ... , 32 types, 32 molecules RdDFKMPQSTUZcfABCEGHIJLNOVWXYabe

#1: 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
#3: Protein 40S ribosomal protein S29 / / Small ribosomal subunit protein uS14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273
#4: 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
#5: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: Protein 40S ribosomal protein S28 / / Small ribosomal subunit protein eS28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#15: Protein 40S ribosomal protein S27a / Ribosome / Ubiquitin carboxyl extension protein 80 / Ubiquitin-40S ribosomal protein S27a


Mass: 17083.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5RKT7
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: 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
#29: 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
#30: 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
#31: Protein 40S ribosomal protein S24 / / Small ribosomal subunit protein eS24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#32: Protein 40S ribosomal protein S26 / / Small ribosomal subunit protein eS26


Mass: 11776.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#33: Protein 40S ribosomal protein S27 / / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#34: Protein 40S ribosomal protein S30 / / Small ribosomal subunit protein eS30


Mass: 6668.938 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 , 2 types, 2 molecules g1

#16: 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: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244
#36: Protein SARS-COV-2 Nsp1 / non-structural protein 1


Mass: 19801.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTD1

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

#2: RNA chain 40S ribosomal rRNA18S


Mass: 602432.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 337376
#35: 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, 4 molecules

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


Mass: 24.305 Da / Num. of mol.: 1 / 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
1complex of SARS-CoV-2 Nsp1 and human 40S ribosomeCOMPLEX#1-#2, #4-#14, #16-#31, #33-#360MULTIPLE SOURCES
2human 40S ribosomeRIBOSOME#1-#2, #4-#14, #16-#31, #33-#351NATURAL
3SARS-CoV-2 Nsp1COMPLEX#361NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Severe acute respiratory syndrome coronavirus 22697049
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 794651 / Symmetry type: POINT

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