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- PDB-6zlw: SARS-CoV-2 Nsp1 bound to the human 40S ribosomal subunit -

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Basic information

Entry
Database: PDB / ID: 6zlw
TitleSARS-CoV-2 Nsp1 bound to the human 40S ribosomal subunit
Components
  • (40S ribosomal protein ...) x 31
  • 18S ribosomal RNA
  • 60S ribosomal protein L41
  • Non-structural protein 1
  • Receptor of activated protein C kinase 1
  • Ubiquitin-40S ribosomal protein S27a
KeywordsVIRAL PROTEIN / Translational Inhibition / SARS-CoV-2 / Immune Evasion / Human Ribosome
Function / homology
Function and homology information


response to TNF agonist / negative regulation of DNA repair / positive regulation of base-excision repair / positive regulation of DNA N-glycosylase activity / oxidized pyrimidine DNA binding / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein tyrosine kinase inhibitor activity ...response to TNF agonist / negative regulation of DNA repair / positive regulation of base-excision repair / positive regulation of DNA N-glycosylase activity / oxidized pyrimidine DNA binding / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation / NF-kappaB complex / positive regulation of Golgi to plasma membrane protein transport / response to extracellular stimulus / ubiquitin ligase inhibitor activity / negative regulation of RNA splicing / IRE1-RACK1-PP2A complex / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / regulation of cell division / positive regulation of endodeoxyribonuclease activity / oxidized purine DNA binding / protein kinase A binding / signaling adaptor activity / negative regulation of endoplasmic reticulum unfolded protein response / negative regulation of ubiquitin protein ligase activity / supercoiled DNA binding / negative regulation of hydrogen peroxide-induced neuron death / ubiquitin-like protein conjugating enzyme binding / positive regulation of ceramide biosynthetic process / erythrocyte homeostasis / negative regulation of phagocytosis / 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 / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / positive regulation of mitochondrial depolarization / phagocytic cup / rescue of stalled ribosome / DNA-(apurinic or apyrimidinic site) lyase / positive regulation of activated T cell proliferation / ion channel inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of cellular component movement / fibroblast growth factor binding / iron-sulfur cluster 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) / stress granule assembly / positive regulation of apoptotic signaling pathway / poly(U) RNA binding / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / monocyte chemotaxis / positive regulation of interleukin-2 production / positive regulation of ubiquitin-protein transferase activity / maturation of SSU-rRNA / BH3 domain binding / regulation of translational fidelity / positive regulation of cyclic-nucleotide phosphodiesterase activity / spindle assembly / ribosomal small subunit export from nucleus / TOR signaling / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of JUN kinase activity / negative regulation of protein kinase B signaling / small-subunit processome / negative regulation of ubiquitin-dependent protein catabolic process / gastrulation / SRP-dependent cotranslational protein targeting to membrane / negative regulation of respiratory burst involved in inflammatory response / positive regulation of microtubule polymerization / ribosomal small subunit biogenesis / SARS coronavirus main proteinase / induction by virus of catabolism of host mRNA / polysome / translation initiation factor binding / molecular adaptor activity / suppression by virus of host ISG15 activity / exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / positive regulation of DNA repair / Hsp70 protein binding / suppression by virus of host NF-kappaB transcription factor activity / innate immune response in mucosa / modulation by virus of host protein ubiquitination / erythrocyte differentiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / viral transcription / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / laminin binding / positive regulation of cell cycle / tubulin binding / polysomal ribosome / negative regulation of peptidyl-serine phosphorylation / negative regulation of protein ubiquitination / positive regulation of intrinsic apoptotic signaling pathway / endodeoxyribonuclease activity / translational initiation
Ribosomal protein S4/S9, eukaryotic/archaeal / Non-structural protein NSP1, betacoronavirus / Ribosomal protein S30 / Ribosomal protein S15P / Ribosomal protein S4/S9 / DPUP/SUD, C-terminal, betacoronavirus / Ribosomal protein L41 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Peptidase C30, coronavirus / Ribosomal protein S19 conserved site ...Ribosomal protein S4/S9, eukaryotic/archaeal / Non-structural protein NSP1, betacoronavirus / Ribosomal protein S30 / Ribosomal protein S15P / Ribosomal protein S4/S9 / DPUP/SUD, C-terminal, betacoronavirus / Ribosomal protein L41 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Peptidase C30, coronavirus / Ribosomal protein S19 conserved site / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Peptidase S1, PA clan / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / K homology domain superfamily, prokaryotic type / Ribosomal protein S17, conserved site / Ribosomal protein S19, superfamily / Ribosomal protein S7 domain / Ubiquitin conserved site / 40S ribosomal protein S1/3, eukaryotes / 50S ribosomal protein L30e-like / Ribosomal protein S5, N-terminal, conserved site / S-adenosyl-L-methionine-dependent methyltransferase / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S5/S7, eukaryotic/archaeal / 40S ribosomal protein SA / Ribosomal protein S10, eukaryotic/archaeal / Non-structural protein NSP3, N-terminal, betacoronavirus / KOW / Ribosomal protein S2, eukaryotic / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S12/S23 / P-loop containing nucleoside triphosphate hydrolase / Non-structural protein NSP3, single-stranded poly(A) binding domain, betacoronavirus / Ubiquitin domain / WD40 repeat, conserved site / 40S ribosomal protein S4, C-terminal domain / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Ribosomal protein S13, conserved site / Non-structural protein NSP9, coronavirus / in:ipr014827: / Non-structural protein NSP7, coronavirus / Non-structural protein NSP8, coronavirus-like / Ribosomal protein S10, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S5, eukaryotic/archaeal / K homology domain-like, alpha/beta / Ribosomal protein S4e, N-terminal, conserved site / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Ribosomal protein S6, eukaryotic / Ribosomal protein S4e, central region / S15/NS1, RNA-binding / Ribosomal protein S3, conserved site / Non-structural protein NSP16, coronavirus-like / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP15, coronavirus / Ribosomal protein S8e, conserved site / Ribosomal protein S6e, conserved site / RNA polymerase, N-terminal, coronaviral / Ribosomal protein S3Ae, conserved site / Ribosomal protein S13-like, H2TH / Ribosomal protein S17e, conserved site / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S21e, conserved site / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein S5, N-terminal / Ribosomal protein S4e, N-terminal / Ribosomal protein S19e, conserved site / Ubiquitin-like domain superfamily / Ribosomal protein S19A/S15e / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Ribosomal protein S2 / Ribosomal protein S10 / WD40 repeat / Ribosomal protein S3Ae / Ribosomal protein S6e / Ribosomal protein S4, KOW domain / Ribosomal protein S3, C-terminal / S27a-like superfamily / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S21e superfamily / Ribosomal protein S26e superfamily / Ribosomal protein S19e / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Ribosomal protein S17e / Ribosomal protein S4e, central domain superfamily / Polyprotein cleavage domain PL2pro superfamily, coronavirus
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 S30 / 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 S30 / 40S ribosomal protein S25 / 40S ribosomal protein S26 / 40S ribosomal protein S28 / 60S ribosomal protein L41 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S21 / Receptor of activated protein C kinase 1 / 40S ribosomal protein S23 / 40S ribosomal protein S18 / 40S ribosomal protein S17 / 40S ribosomal protein S14 / 40S ribosomal protein S27 / 40S ribosomal protein SA / 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 speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsThoms, M. / Buschauer, R. / Ameismeier, M. / Denk, T. / Kratzat, H. / Mackens-Kiani, T. / Cheng, J. / Berninghausen, O. / Becker, T. / Beckmann, R.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB/TRR-174 Germany
German Research Foundation (DFG)BE1814/15-1 Germany
German Research Foundation (DFG)BE1814/1-1 Germany
CitationJournal: Science / Year: 2020
Title: Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Authors: Matthias Thoms / Robert Buschauer / Michael Ameismeier / Lennart Koepke / Timo Denk / Maximilian Hirschenberger / Hanna Kratzat / Manuel Hayn / Timur Mackens-Kiani / Jingdong Cheng / Jan H ...Authors: Matthias Thoms / Robert Buschauer / Michael Ameismeier / Lennart Koepke / Timo Denk / Maximilian Hirschenberger / Hanna Kratzat / Manuel Hayn / Timur Mackens-Kiani / Jingdong Cheng / Jan H Straub / Christina M Stürzel / Thomas Fröhlich / Otto Berninghausen / Thomas Becker / Frank Kirchhoff / Konstantin M J Sparrer / Roland Beckmann /
Abstract: SARS-CoV-2 is the causative agent of the current COVID-19 pandemic. A major virulence factor of SARS-CoVs is the nonstructural protein 1 (Nsp1) which suppresses host gene expression by ribosome ...SARS-CoV-2 is the causative agent of the current COVID-19 pandemic. A major virulence factor of SARS-CoVs is the nonstructural protein 1 (Nsp1) which suppresses host gene expression by ribosome association. Here, we show that Nsp1 from SARS-CoV-2 binds to the 40S ribosomal subunit, resulting in shutdown of mRNA translation both in vitro and in cells. Structural analysis by cryo-electron microscopy (cryo-EM) of in vitro reconstituted Nsp1-40S and various native Nsp1-40S and -80S complexes revealed that the Nsp1 C terminus binds to and obstructs the mRNA entry tunnel. Thereby, Nsp1 effectively blocks RIG-I-dependent innate immune responses that would otherwise facilitate clearance of the infection. Thus, the structural characterization of the inhibitory mechanism of Nsp1 may aid structure-based drug design against SARS-CoV-2.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)1,245,11239
Polymers1,244,91536
Non-polymers1963
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area191380 Å2
ΔGint-1456 kcal/mol
Surface area390420 Å2
MethodPISA

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Components

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

#1: 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
#2: 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
#3: 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
#4: Protein 40S ribosomal protein S4, X isoform / Ribosome / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4 / Ribosome


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#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 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
#7: 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
#8: 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
#9: 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
#10: 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
#11: 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
#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 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
#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 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: Protein 40S ribosomal protein S26 / / Small ribosomal subunit protein eS26 /


Mass: 13047.532 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 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
#30: 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
#31: 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

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Protein , 3 types, 3 molecules gji

#32: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979
#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: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244
#36: 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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Protein/peptide / RNA chain / Non-polymers , 3 types, 5 molecules h2

#33: 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
#35: RNA chain 18S ribosomal RNA / /


Mass: 602432.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 337376
#37: 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 bound to the human 40S ribosomal subunitRIBOSOME1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 360MULTIPLE SOURCES
2Human 40S ribosomal subunitCOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 351NATURAL
3SARS-CoV-2 Nsp1COMPLEX361RECOMBINANT
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: 7.5
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 44.8 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 173060 / Symmetry type: POINT

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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