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- PDB-8ppk: Bat-Hp-CoV Nsp1 and eIF1 bound to the human 40S small ribosomal s... -

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Entry
Database: PDB / ID: 8ppk
TitleBat-Hp-CoV Nsp1 and eIF1 bound to the human 40S small ribosomal subunit
Components
  • (40S ribosomal protein ...) x 28
  • (Small ribosomal subunit protein ...) x 3
  • 18S rRNA18S ribosomal RNA
  • 60S ribosomal protein L41
  • Eukaryotic translation initiation factor 1
  • Nsp1Viral nonstructural protein
  • Receptor of activated protein C kinase 1
  • Ubiquitin-40S ribosomal protein S27a
KeywordsTRANSLATION / Nsp1 / MERS / SARS / SARS-CoV2 / ribosome / 40S ribosomal subunit / translation inhibition / coronavirus / 43S PIC / 43S pre-initiation complex / mRNA channel / initiation factor / eIF2 / eIF3 / eIF1 / eIF1A / VIRAL PROTEIN
Function / homology
Function and homology information


positive regulation of mRNA cis splicing, via spliceosome / multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity ...positive regulation of mRNA cis splicing, via spliceosome / multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / eukaryotic 48S preinitiation complex / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / nucleolus organization / : / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / laminin receptor activity / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / neural crest cell differentiation / rRNA modification in the nucleus and cytosol / negative regulation of phagocytosis / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / regulation of translational initiation / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / pigmentation / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / phagocytic cup / positive regulation of mitochondrial depolarization / negative regulation of Wnt signaling pathway / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / fibroblast growth factor binding / regulation of cell division / SARS-CoV-1 modulates host translation machinery / Protein hydroxylation / iron-sulfur cluster binding / TOR signaling / BH3 domain binding / mTORC1-mediated signalling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation / Selenocysteine synthesis / monocyte chemotaxis / cysteine-type endopeptidase activator activity involved in apoptotic process / Formation of a pool of free 40S subunits / ribosomal small subunit export from nucleus / ribosomal small subunit binding / positive regulation of cyclic-nucleotide phosphodiesterase activity / Eukaryotic Translation Termination / organelle membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / translation regulator activity / 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 / negative regulation of respiratory burst involved in inflammatory response / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / host cell membrane / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / endoplasmic reticulum-Golgi intermediate compartment / gastrulation / 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) / rough endoplasmic reticulum / spindle assembly / regulation of translational fidelity / MDM2/MDM4 family protein binding / laminin binding / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / negative regulation of smoothened signaling pathway / rescue of stalled ribosome / signaling adaptor activity / positive regulation of cell cycle / negative regulation of peptidyl-serine phosphorylation / translation initiation factor binding / maturation of SSU-rRNA
Similarity search - Function
Eukaryotic translation initiation factor SUI1 / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / AAA domain / Ubiquitin-like protein FUBI / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus ...Eukaryotic translation initiation factor SUI1 / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / AAA domain / Ubiquitin-like protein FUBI / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / : / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S12e / : / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S19e, conserved site / S27a-like superfamily / Ribosomal protein S26e / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S26e signature. / Ribosomal protein S17e, conserved site / : / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / Ribosomal protein S19A/S15e / Ribosomal protein S21e signature. / Ribosomal protein S30 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal_S17 N-terminal / Plectin/S10, N-terminal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein S7e / Plectin/S10 domain / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / RS4NT (NUC023) domain / Ribosomal protein S27 / Ribosomal S3Ae family / Ribosomal protein S17e signature. / Ribosomal protein S28e / Ribosomal family S4e / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S7e signature. / Ribosomal protein S6e / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e signature.
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / ORF1ab polyprotein / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS3 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / ORF1ab polyprotein / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Eukaryotic translation initiation factor 1 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / 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 uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS28 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1
Similarity search - Component
Biological speciesHomo sapiens (human)
Bat Hp-betacoronavirus/Zhejiang2013
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsSchubert, K. / Karousis, E.D. / Ban, I. / Lapointe, C.P. / Leibundgut, M. / Baeumlin, E. / Kummerant, E. / Scaiola, A. / Schoenhut, T. / Ziegelmueller, J. ...Schubert, K. / Karousis, E.D. / Ban, I. / Lapointe, C.P. / Leibundgut, M. / Baeumlin, E. / Kummerant, E. / Scaiola, A. / Schoenhut, T. / Ziegelmueller, J. / Puglisi, J.D. / Muehlemann, O. / Ban, N.
Funding support Switzerland, United States, 13items
OrganizationGrant numberCountry
Swiss National Science Foundation182341 Switzerland
Swiss National Science Foundation182831 Switzerland
Swiss National Science Foundation204161 Switzerland
Swiss National Science Foundation51NF40-182880 Switzerland
Swiss National Science Foundation51NF40--205601 Switzerland
Other governmentETH-23 18-2 Switzerland
Other government Switzerland
Other private Switzerland
Other private Switzerland
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM011378 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM145306 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG064690 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM144678 United States
Citation
Journal: Mol Cell / Year: 2023
Title: Universal features of Nsp1-mediated translational shutdown by coronaviruses.
Authors: Katharina Schubert / Evangelos D Karousis / Ivo Ban / Christopher P Lapointe / Marc Leibundgut / Emilie Bäumlin / Eric Kummerant / Alain Scaiola / Tanja Schönhut / Jana Ziegelmüller / ...Authors: Katharina Schubert / Evangelos D Karousis / Ivo Ban / Christopher P Lapointe / Marc Leibundgut / Emilie Bäumlin / Eric Kummerant / Alain Scaiola / Tanja Schönhut / Jana Ziegelmüller / Joseph D Puglisi / Oliver Mühlemann / Nenad Ban /
Abstract: Nonstructural protein 1 (Nsp1) produced by coronaviruses inhibits host protein synthesis. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Nsp1 C-terminal domain was shown to bind the ...Nonstructural protein 1 (Nsp1) produced by coronaviruses inhibits host protein synthesis. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Nsp1 C-terminal domain was shown to bind the ribosomal mRNA channel to inhibit translation, but it is unclear whether this mechanism is broadly used by coronaviruses, whether the Nsp1 N-terminal domain binds the ribosome, or how Nsp1 allows viral RNAs to be translated. Here, we investigated Nsp1 from SARS-CoV-2, Middle East respiratory syndrome coronavirus (MERS-CoV), and Bat-Hp-CoV coronaviruses using structural, biophysical, and biochemical experiments, revealing a conserved role for the C-terminal domain. Additionally, the N-terminal domain of Bat-Hp-CoV Nsp1 binds to the decoding center of the 40S subunit, where it would prevent mRNA and eIF1A accommodation. Structure-based experiments demonstrated the importance of decoding center interactions in all three coronaviruses and showed that the same regions of Nsp1 are necessary for the selective translation of viral RNAs. Our results provide a mechanistic framework to understand how Nsp1 controls preferential translation of viral RNAs.
#1: Journal: Mol.Cell / Year: 2023
Title: Universal features of Nsp1-mediated translational shutdown by coronaviruses
Authors: Schubert, K. / Karousis, E.D. / Ban, I. / Lapointe, C.P. / Leibundgut, M. / Baeumlin, E. / Kummerant, E. / Scaiola, A. / Schoenhut, T. / Ziegelmueller, J. / Puglisi, J.D. / Muehlemann, O. / Ban, N.
History
DepositionJul 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
p: Eukaryotic translation initiation factor 1
2: 18S rRNA
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: Small ribosomal subunit protein uS13
T: Small ribosomal subunit protein eS19
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: Small ribosomal subunit protein eS30
f: Ubiquitin-40S ribosomal protein S27a
g: Receptor of activated protein C kinase 1
h: 60S ribosomal protein L41
j: Nsp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,271,012268
Polymers1,268,11837
Non-polymers2,894231
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 4 molecules pfgj

#1: Protein Eukaryotic translation initiation factor 1 / eIF1 / A121 / Protein translation factor SUI1 homolog / Sui1iso1


Mass: 12752.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF1, SUI1 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL / References: UniProt: P41567
#34: 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 / Details: 1-76: ubiquitin zinc finger protein / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62979
#35: 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) / Cell line: HEK293E / References: UniProt: P63244
#37: Protein Nsp1 / Viral nonstructural protein


Mass: 21172.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: residues 1-174 of Bat-Hp-betacoronavirus/Zhejiang2013 polyprotein ORF1ab
Source: (gene. exp.) Bat Hp-betacoronavirus/Zhejiang2013 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL / References: UniProt: A0A088DIE1

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40S ribosomal protein ... , 28 types, 28 molecules ABCDEFGHIJKLMNOPQRUVWXYZabcd

#3: 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: 32925.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: S2: acetylserine (SAC) / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P08865
#4: 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) / Cell line: HEK293E / References: UniProt: P61247
#5: 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) / Cell line: HEK293E / References: UniProt: P15880
#6: 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) / Cell line: HEK293E
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#7: 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) / Cell line: HEK293E / References: UniProt: P62701
#8: 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) / Cell line: HEK293E / References: UniProt: P46782
#9: 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) / Cell line: HEK293E / References: UniProt: P62753
#10: 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) / Cell line: HEK293E / References: UniProt: P62081
#11: 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) / Cell line: HEK293E / References: UniProt: P62241
#12: 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) / Cell line: HEK293E / References: UniProt: P46781
#13: 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) / Cell line: HEK293E / References: UniProt: P46783
#14: 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) / Cell line: HEK293E / References: UniProt: P62280
#15: 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) / Cell line: HEK293E / References: UniProt: P25398
#16: 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) / Cell line: HEK293E / References: UniProt: P62277
#17: 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 / Details: D138: isoaspartate (IAS) / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62263
#18: 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) / Cell line: HEK293E / References: UniProt: P62841
#19: 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) / Cell line: HEK293 / References: UniProt: P62249
#20: 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) / Cell line: HEK293E / References: UniProt: P08708
#23: 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
#24: Protein 40S ribosomal protein S21 / / Small ribosomal subunit protein eS21


Mass: 9166.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: M1: acetylmethionine (AME) / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P63220
#25: 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) / Cell line: HEK293E / References: UniProt: P62244
#26: Protein 40S ribosomal protein S23 /


Mass: 15860.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P62: hydroxyproline (HY3) / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: A0A4W2DI10
#27: 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) / Cell line: HEK293E / References: UniProt: P62847
#28: 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) / Cell line: HEK293E / References: UniProt: P62851
#29: 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 / Details: zinc finger protein / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62854
#30: 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) / Cell line: HEK293E / References: UniProt: P42677
#31: 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) / Cell line: HEK293E / References: UniProt: P62857
#32: 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 / Details: zinc finger protein / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62273

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Small ribosomal subunit protein ... , 3 types, 3 molecules STe

#21: Protein Small ribosomal subunit protein uS13 / 40S ribosomal protein S18 / Ke-3 / Ke3


Mass: 17801.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: S2: acetylserine (SAC) / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62269
#22: Protein Small ribosomal subunit protein eS19 / 40S ribosomal protein S19


Mass: 16104.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: R67: omega-methylarginine (NMM) / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P39019
#33: Protein Small ribosomal subunit protein eS30 / 40S ribosomal protein S30


Mass: 14415.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 1-74: ubiquitin / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62861

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

#2: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 603609.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: unmodified rRNA sequence: >18S_rRNA_taoka_unmodified UACCUGGUUGAUCCUGCCAGUAGCAUaUGCUUGuCuCAAAGAUUAAGCCAUGCAUGUCUA AGUACGCACGGCCGGUACAGUGAAACUGCGAAuGGCUCaUUAAAuCAGuUAUGGUuCCuU ...Details: unmodified rRNA sequence: >18S_rRNA_taoka_unmodified UACCUGGUUGAUCCUGCCAGUAGCAUaUGCUUGuCuCAAAGAUUAAGCCAUGCAUGUCUA AGUACGCACGGCCGGUACAGUGAAACUGCGAAuGGCUCaUUAAAuCAGuUAUGGUuCCuU uGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAaUUCUAGaGCUAAuAcAUGCCG ACGGGCGCUGACCCCCUUCGCGGGGGGGAuGCGUGCAuUUAUCAGAUCAAAACCAACCCG GUCAGCCCCUCUCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCUUUGGUGACUCuAGAU AACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCuGCCCUA UCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGuGACGGGGAAUCAGG GUUCGAUuCCGGAGAgGGAGCCUGAGAAACGGCUACCACAUcCAAGGaAGGCAGCAGGCG CGCaAAUUACCCACUCCCGACCCGGGGAgGUaGUGAcGAAAAAUAACAAUACAGGACUCU UUCGAGGCCCUGUAAUUGGAAUGAGUCCACUuUAAaUCCUUUAACGAGGaUCCAUUGGAG gGCAAGUCuGGUGCCAGCAGcCGCGGuAAUUCCAGCUCCAAUAgCGUAuAuUAAAGUUGC UGCAGUUaAAAAGCUCGUAGuUgGAuCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGA GCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGU CCCGCGGGGCCCGAAGcGuUuACUUUGAAAAAAuuAGAGUGuUCAAAGCAGGCCCGAGCC GCCUGGAUACCGCAGCUAGGAAuAAugGAAUAGGACCGCGGUUCUAUUUUGUUGGUuUUC GGAACUGAGGCCAUGAUuAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGU GAAAUuCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUuGCCAAGAAUGUUUUCA UUAAUCAAGAaCGAAAGUCGGAGGuuCGAAGACGAuCAGAUACCGUCGUAGUUCCGACCA uAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCuUCCG GGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAuGGuUGCAAAGCUGAAACUUAAAGGAA UUGACGGAAGGGCACCACCAGGAGUGGAGCCuGCGGCuUAAUUuGACuCAACACGGGAAA CCUCACCCGGCcCGGACACGGACAGGAuUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUG GGUGGuGgUGCAUGGCcGUUCUUAGUuGGUGGAGCGAUUUGUCUGGuUAAUUCCGAUAAC GAaCGAGACUcUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAAC UuCUuAgAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAgGUCUGUGAUG CCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCU ACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAA UUAUuCCCCAUGAACGAGgAAUuCCCAGUAAGUGCGGGUCAUAAGCUuGCGUUGAUUaAG UCCCUGCCCUUuGUACACACCGcCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCC UCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGA ACUuGACUAUCUAGAGGAAGUAAAAGUCGUAaCAAGGUUUCcGUAGGUGaaCCUGCGGAA GGAUCAUUA
Source: (natural) Homo sapiens (human) / Cell line: HEK293E
#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
Details: large subunit protein associated with small subunit
Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62945

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Non-polymers , 3 types, 231 molecules

#38: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 117 / Source method: obtained synthetically
#39: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 111 / Source method: obtained synthetically / Formula: Mg
#40: Chemical ChemComp-ZN / ZINC ION


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

ComponentName: Bat-Hp-CoV Nsp1 - eIF1 - 40S complex / Type: RIBOSOME / Entity ID: #1-#37 / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameBuffer-ID
150 mMHEPES-KOH1
2100 mMKOAc1
310 mMMg(OAc)21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: f.c. 80 nM
Specimen supportDetails: 15 mA easiGlow Discharge cleaning system (PELCO) / Grid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 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 / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 12607

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Processing

EM software
IDNameVersionCategoryDetails
7Coot0.9.8.5model fitting
9PHENIX1.20.1model refinementphenix.real_space_refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98750 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: phenix.real_space_refine
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeDetailsInitial refinement model-ID
16ZOK

6zok

6ZOK40S body1
26ZOL

6zol

6ZOL40S head2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00284487
ELECTRON MICROSCOPYf_angle_d0.409122520
ELECTRON MICROSCOPYf_dihedral_angle_d13.28237709
ELECTRON MICROSCOPYf_chiral_restr0.0315025
ELECTRON MICROSCOPYf_plane_restr0.0038979

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