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- PDB-6zmo: SARS-CoV-2 Nsp1 bound to the human LYAR-80S-eEF1a ribosome complex -

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Basic information

Entry
Database: PDB / ID: 6zmo
TitleSARS-CoV-2 Nsp1 bound to the human LYAR-80S-eEF1a ribosome complex
Components
  • (40S ribosomal protein ...) x 31
  • (60S ribosomal protein ...) x 43
  • (tRNATransfer RNA) x 2
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • Cell growth-regulating nucleolar protein
  • Elongation factor 1-alpha 1
  • Non-structural protein 1
  • Proliferation-associated protein 2G4
  • Receptor of activated protein C kinase 1
  • Ubiquitin-40S ribosomal protein S27a
  • Ubiquitin-60S ribosomal protein L40
KeywordsVIRAL PROTEIN / Translational Inhibition / SARS-CoV-2 / Immune Evasion / Human Ribosome
Function / homology
Function and homology information


cytoplasmic side of lysosomal membrane / regulation of D-erythro-sphingosine kinase activity / regulation of chaperone-mediated autophagy / eukaryotic translation elongation factor 1 complex / regulation of translation at presynapse, modulating synaptic transmission / negative regulation of formation of translation preinitiation complex / positive regulation of selenocysteine incorporation / optic nerve development / eukaryotic 80S initiation complex / negative regulation of protein neddylation ...cytoplasmic side of lysosomal membrane / regulation of D-erythro-sphingosine kinase activity / regulation of chaperone-mediated autophagy / eukaryotic translation elongation factor 1 complex / regulation of translation at presynapse, modulating synaptic transmission / negative regulation of formation of translation preinitiation complex / positive regulation of selenocysteine incorporation / optic nerve development / eukaryotic 80S initiation complex / negative regulation of protein neddylation / 5.8S rRNA binding / TORC2 complex binding / negative regulation of innate immune response / positive regulation of signal transduction by p53 class mediator / axial mesoderm development / ribosomal protein import into nucleus / protein-DNA complex disassembly / middle ear morphogenesis / transcription regulator inhibitor activity / 90S preribosome assembly / selenocysteine insertion sequence binding / GAIT complex / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation / positive regulation of Golgi to plasma membrane protein transport / positive regulation of transcription by RNA polymerase I / response to extracellular stimulus / exit from mitosis / negative regulation of RNA splicing / IRE1-RACK1-PP2A complex / ubiquitin ligase inhibitor activity / laminin receptor activity / retinal ganglion cell axon guidance / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of cell division / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / regulation of translation involved in cellular response to UV / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / alpha-beta T cell differentiation / negative regulation of endoplasmic reticulum unfolded protein response / negative regulation of hydrogen peroxide-induced neuron death / A band / negative regulation of DNA repair / positive regulation of DNA N-glycosylase activity / oxidized pyrimidine DNA binding / positive regulation of base-excision repair / response to TNF agonist / 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 / mammalian oogenesis stage / NF-kappaB complex / negative regulation of phagocytosis / cytosolic ribosome / regulation of establishment of cell polarity / positive regulation of endodeoxyribonuclease activity / signaling adaptor activity / negative regulation of Wnt signaling pathway / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / protein targeting to peroxisome / activation-induced cell death of T cells / protein kinase A binding / cortical actin cytoskeleton / positive regulation of mitochondrial depolarization / supercoiled DNA binding / translation regulator activity / translational elongation / 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 / photoreceptor outer segment / blastocyst development / ribonucleoprotein complex assembly / ubiquitin-like protein conjugating enzyme binding / iron-sulfur cluster binding / 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 / bone development / positive regulation of T cell receptor signaling pathway / poly(U) RNA binding / stress granule assembly / 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of activated T cell proliferation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / GABA-ergic synapse
Betacoronavirus replicase NSP1 / Ribosomal protein S10, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L10e, conserved site / Ribosomal protein L13e, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L32e, conserved site ...Betacoronavirus replicase NSP1 / Ribosomal protein S10, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L10e, conserved site / Ribosomal protein L13e, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S8e, conserved site / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Ribosomal protein L7Ae/L8/Nhp2 family / RNA synthesis protein NSP10, coronavirus / Ribosomal protein S5, N-terminal, conserved site / Ribosomal S11, conserved site / Ribosomal protein L3, conserved site / Non-structural protein NSP7, coronavirus / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Peptidase C16, coronavirus / Ribosomal protein L25/L23 / Ribosomal protein S5, N-terminal / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Ribosomal protein L2, domain 3 / Non-structural protein NSP9, coronavirus / Non-structural protein NSP8, coronavirus-like / Ribosomal S24e conserved site / Zinc finger, C2H2, LYAR-type / WD40/YVTN repeat-like-containing domain superfamily / K homology domain-like, alpha/beta / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L10e/L16 / WD40-repeat-containing domain / Ribosomal protein L30, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein S4, conserved site / WD40 repeat, conserved site / Ubiquitin conserved site / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein L2, archaeal-type / Ribosomal protein S15P / in:ipr023106: / Ribosomal protein L24e, conserved site / Ribosomal protein L13, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L4 domain superfamily / Ribosomal protein S19/S15, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein L39e domain superfamily / Ribosomal protein L19/L19e conserved site / Ribosomal protein L1, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L1-like / Ribosomal protein S7 domain / Non-structural protein NSP3, N-terminal, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Ribosomal protein L15e core domain superfamily / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / 60S ribosomal protein L4, C-terminal domain / (+) RNA virus helicase core domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / P-loop containing nucleoside triphosphate hydrolase / 30s ribosomal protein S13, C-terminal / Ribosomal protein L30e, conserved site / Ribosomal protein S4/S9 / Ubiquitin domain / Ribosomal protein L11, N-terminal / Ribosomal protein L14P, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein L23 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L31e, conserved site / Ribosomal protein L39e, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein L11, C-terminal / Ribosomal protein L11, conserved site / DPUP/SUD, C-terminal, betacoronavirus / Ribosomal protein L15e, conserved site / Ribosomal protein L5, conserved site
60S ribosomal protein L8 / gb:555853: / 60S ribosomal protein L34 / 60S ribosomal protein L5 / 60S ribosomal protein L21 / 60S ribosomal protein L28 / 40S ribosomal protein S9 / 40S ribosomal protein S5 / 40S ribosomal protein S10 / 60S ribosomal protein L29 ...60S ribosomal protein L8 / gb:555853: / 60S ribosomal protein L34 / 60S ribosomal protein L5 / 60S ribosomal protein L21 / 60S ribosomal protein L28 / 40S ribosomal protein S9 / 40S ribosomal protein S5 / 40S ribosomal protein S10 / 60S ribosomal protein L29 / 60S ribosomal protein L14 / 60S ribosomal protein L35 / 40S ribosomal protein S20 / 40S ribosomal protein S3a / 60S ribosomal protein L26 / 60S ribosomal protein L15 / 60S ribosomal protein L37a / 60S ribosomal protein L37 / 40S ribosomal protein S7 / 40S ribosomal protein S8 / 60S ribosomal protein L27a / 40S ribosomal protein S27 / 40S ribosomal protein S16 / 60S ribosomal protein L17 / 60S acidic ribosomal protein P0 / 40S ribosomal protein S17 / 40S ribosomal protein SA / Replicase polyprotein 1ab / 40S ribosomal protein S2 / 60S ribosomal protein L35a / 60S ribosomal protein L7 / 40S ribosomal protein S3 / 60S ribosomal protein L13a / 40S ribosomal protein S12 / 60S ribosomal protein L13 / 60S ribosomal protein L12 / 60S ribosomal protein L9 / 60S ribosomal protein L22 / 60S ribosomal protein L4 / 40S ribosomal protein S19 / 60S ribosomal protein L3 / 40S ribosomal protein S15a / 40S ribosomal protein S14 / gb:23898: / 60S ribosomal protein L36a / Ubiquitin-40S ribosomal protein S27a / Ubiquitin-60S ribosomal protein L40 / 60S ribosomal protein L38 / 40S ribosomal protein S21 / Receptor of activated protein C kinase 1 / Elongation factor 1-alpha 1 / 60S ribosomal protein L24 / 60S ribosomal protein L19 / 60S ribosomal protein L11 / 60S ribosomal protein L18a / 60S ribosomal protein L6 / 60S ribosomal protein L18 / 60S ribosomal protein L10-like / Cell growth-regulating nucleolar protein / Proliferation-associated protein 2G4 / 60S ribosomal protein L36 / gb:nr_145822.1: / 60S ribosomal protein L41 / 60S ribosomal protein L32 / 40S ribosomal protein S23 / 60S ribosomal protein L23 / 40S ribosomal protein S18 / 40S ribosomal protein S29 / 40S ribosomal protein S13 / 40S ribosomal protein S11 / 60S ribosomal protein L7a / 40S ribosomal protein S4, X isoform / 60S ribosomal protein L23a / 40S ribosomal protein S6 / 40S ribosomal protein S15 / 60S ribosomal protein L10a / 40S ribosomal protein S24 / 40S ribosomal protein S25 / 40S ribosomal protein S26 / 40S ribosomal protein S28 / 40S ribosomal protein S30 / 60S ribosomal protein L30 / 60S ribosomal protein L39 / 60S ribosomal protein L31 / 60S ribosomal protein L27
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 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: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current coronavirus disease 2019 (COVID-19) pandemic. A major virulence factor of SARS-CoVs is the ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current coronavirus disease 2019 (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 40 ribosomal subunit, resulting in shutdown of messenger RNA (mRNA) translation both in vitro and in cells. Structural analysis by cryo-electron microscopy of in vitro-reconstituted Nsp1-40 and various native Nsp1-40 and -80 complexes revealed that the Nsp1 C terminus binds to and obstructs the mRNA entry tunnel. Thereby, Nsp1 effectively blocks retinoic acid-inducible gene 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 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 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

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Structure visualization

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Assembly

Deposited unit
L5: 28S ribosomal RNA
L7: 5S ribosomal RNA
L8: 5.8S ribosomal RNA
LA: 60S ribosomal protein L8
LB: 60S ribosomal protein L3
LC: 60S ribosomal protein L4
LD: 60S ribosomal protein L5
LE: 60S ribosomal protein L6
LF: 60S ribosomal protein L7
LG: 60S ribosomal protein L7a
LH: 60S ribosomal protein L9
LI: 60S ribosomal protein L10-like
LJ: 60S ribosomal protein L11
LL: 60S ribosomal protein L13
LM: 60S ribosomal protein L14
LN: 60S ribosomal protein L15
LO: 60S ribosomal protein L13a
LP: 60S ribosomal protein L17
LQ: 60S ribosomal protein L18
LR: 60S ribosomal protein L19
LS: 60S ribosomal protein L18a
LT: 60S ribosomal protein L21
LU: 60S ribosomal protein L22
LV: 60S ribosomal protein L23
LW: 60S ribosomal protein L24
LX: 60S ribosomal protein L23a
LY: 60S ribosomal protein L26
LZ: 60S ribosomal protein L27
La: 60S ribosomal protein L27a
Lb: 60S ribosomal protein L29
Lc: 60S ribosomal protein L30
Ld: 60S ribosomal protein L31
Le: 60S ribosomal protein L32
Lf: 60S ribosomal protein L35a
Lg: 60S ribosomal protein L34
Lh: 60S ribosomal protein L35
Li: 60S ribosomal protein L36
Lj: 60S ribosomal protein L37
Lk: 60S ribosomal protein L38
Ll: 60S ribosomal protein L39
Lm: Ubiquitin-60S ribosomal protein L40
Ln: 60S ribosomal protein L41
Lo: 60S ribosomal protein L36a
Lp: 60S ribosomal protein L37a
Lr: 60S ribosomal protein L28
Ls: 60S acidic ribosomal protein P0
Lt: 60S ribosomal protein L12
Lz: 60S ribosomal protein L10a
S2: 18S ribosomal RNA
SA: 40S ribosomal protein SA
SB: 40S ribosomal protein S3a
SD: 40S ribosomal protein S3
SE: 40S ribosomal protein S4, X isoform
SF: 40S ribosomal protein S5
SH: 40S ribosomal protein S7
SI: 40S ribosomal protein S8
SK: 40S ribosomal protein S10
SL: 40S ribosomal protein S11
SP: 40S ribosomal protein S15
SQ: 40S ribosomal protein S16
SR: 40S ribosomal protein S17
SS: 40S ribosomal protein S18
ST: 40S ribosomal protein S19
SU: 40S ribosomal protein S20
SV: 40S ribosomal protein S21
SX: 40S ribosomal protein S23
Sa: 40S ribosomal protein S26
Sc: 40S ribosomal protein S28
Sd: 40S ribosomal protein S29
Sg: Receptor of activated protein C kinase 1
SC: 40S ribosomal protein S2
SG: 40S ribosomal protein S6
SJ: 40S ribosomal protein S9
SM: 40S ribosomal protein S12
SN: 40S ribosomal protein S13
SO: 40S ribosomal protein S14
SW: 40S ribosomal protein S15a
SY: 40S ribosomal protein S24
SZ: 40S ribosomal protein S25
Sb: 40S ribosomal protein S27
Se: 40S ribosomal protein S30
Sf: Ubiquitin-40S ribosomal protein S27a
CA: Proliferation-associated protein 2G4
CB: tRNA
CC: tRNA
CD: Elongation factor 1-alpha 1
CE: Cell growth-regulating nucleolar protein
i: Non-structural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,072,341352
Polymers4,065,59688
Non-polymers6,745264
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 6 types, 6 molecules L5L7L8S2CBCC

#1: RNA chain 28S ribosomal RNA /


Mass: 1638922.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: NR_145822.1
#2: RNA chain 5S ribosomal RNA /


Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 23898
#3: RNA chain 5.8S ribosomal RNA /


Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 555853
#49: RNA chain 18S ribosomal RNA /


Mass: 602793.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#84: RNA chain tRNA / Transfer RNA


Mass: 28053.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#85: RNA chain tRNA / Transfer RNA


Mass: 24004.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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60S ribosomal protein ... , 43 types, 43 molecules LALBLCLDLELFLGLHLILJLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLe...

#4: Protein 60S ribosomal protein L8 / / Large ribosomal subunit protein uL2


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62917
#5: Protein 60S ribosomal protein L3 / / HIV-1 TAR RNA-binding protein B / TARBP-B / Large ribosomal subunit protein uL3


Mass: 46211.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39023
#6: Protein 60S ribosomal protein L4 / / 60S ribosomal protein L1 / Large ribosomal subunit protein uL4


Mass: 47804.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36578
#7: Protein 60S ribosomal protein L5 / / Large ribosomal subunit protein uL18


Mass: 34426.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46777
#8: Protein 60S ribosomal protein L6 / / Large ribosomal subunit protein eL6 / Neoplasm-related protein C140 / Tax-responsive enhancer ...Large ribosomal subunit protein eL6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding protein 107 / TaxREB107


Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02878
#9: Protein 60S ribosomal protein L7 / / Large ribosomal subunit protein uL30


Mass: 29290.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124
#10: Protein 60S ribosomal protein L7a / / Large ribosomal subunit protein eL8 / PLA-X polypeptide / Surfeit locus protein 3


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62424
#11: Protein 60S ribosomal protein L9 / / Large ribosomal subunit protein uL6


Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P32969
#12: Protein 60S ribosomal protein L10-like / / Large ribosomal subunit protein uL16-like


Mass: 24570.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96L21
#13: Protein 60S ribosomal protein L11 / / CLL-associated antigen KW-12 / Large ribosomal subunit protein uL5


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62913
#14: Protein 60S ribosomal protein L13 / / Breast basic conserved protein 1 / Large ribosomal subunit protein eL13


Mass: 24321.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P26373
#15: Protein 60S ribosomal protein L14 / / CAG-ISL 7 / Large ribosomal subunit protein eL14


Mass: 23485.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50914
#16: Protein 60S ribosomal protein L15 / / Large ribosomal subunit protein eL15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61313
#17: Protein 60S ribosomal protein L13a / / 23 kDa highly basic protein / Large ribosomal subunit protein uL13


Mass: 23633.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40429
#18: Protein 60S ribosomal protein L17 / / 60S ribosomal protein L23 / Large ribosomal subunit protein uL22 / PD-1


Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18621
#19: Protein 60S ribosomal protein L18 / / Large ribosomal subunit protein eL18


Mass: 21687.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q07020
#20: Protein 60S ribosomal protein L19 / / Large ribosomal subunit protein eL19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P84098
#21: Protein 60S ribosomal protein L18a / / Large ribosomal subunit protein eL20


Mass: 20808.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02543
#22: Protein 60S ribosomal protein L21 / / Large ribosomal subunit protein eL21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46778
#23: Protein 60S ribosomal protein L22 / / EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding ...EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding protein HBp15 / Large ribosomal subunit protein eL22


Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35268
#24: Protein 60S ribosomal protein L23 / / 60S ribosomal protein L17 / Large ribosomal subunit protein uL14


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62829
#25: Protein 60S ribosomal protein L24 / / 60S ribosomal protein L30 / Large ribosomal subunit protein eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83731
#26: Protein 60S ribosomal protein L23a / / Large ribosomal subunit protein uL23


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62750
#27: Protein 60S ribosomal protein L26 / / Large ribosomal subunit protein uL24


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61254
#28: Protein 60S ribosomal protein L27 / / Large ribosomal subunit protein eL27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61353
#29: Protein 60S ribosomal protein L27a / / Large ribosomal subunit protein uL15


Mass: 16604.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46776
#30: Protein 60S ribosomal protein L29 / / Cell surface heparin-binding protein HIP / Large ribosomal subunit protein eL29


Mass: 17804.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P47914
#31: Protein 60S ribosomal protein L30 / / Large ribosomal subunit protein eL30


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62888
#32: Protein 60S ribosomal protein L31 / / Large ribosomal subunit protein eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62899
#33: Protein 60S ribosomal protein L32 / / Large ribosomal subunit protein eL32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62910
#34: Protein 60S ribosomal protein L35a / / Cell growth-inhibiting gene 33 protein / Large ribosomal subunit protein eL33


Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18077
#35: Protein 60S ribosomal protein L34 / / Large ribosomal subunit protein eL34


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49207
#36: Protein 60S ribosomal protein L35 / / Large ribosomal subunit protein uL29


Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42766
#37: Protein 60S ribosomal protein L36 / / Large ribosomal subunit protein eL36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3U8
#38: Protein 60S ribosomal protein L37 / / G1.16 / Large ribosomal subunit protein eL37


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61927
#39: Protein 60S ribosomal protein L38 / / Large ribosomal subunit protein eL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63173
#40: Protein 60S ribosomal protein L39 / / Large ribosomal subunit protein eL39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62891
#42: 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
#43: Protein 60S ribosomal protein L36a / / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 ...60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 protein / Large ribosomal subunit protein eL42


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83881
#44: Protein 60S ribosomal protein L37a / / Large ribosomal subunit protein eL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61513
#45: Protein 60S ribosomal protein L28 / / Large ribosomal subunit protein eL28


Mass: 15784.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46779
#47: Protein 60S ribosomal protein L12 / / Large ribosomal subunit protein uL11


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P30050
#48: Protein 60S ribosomal protein L10a / / CSA-19 / Large ribosomal subunit protein uL1 / Neural precursor cell expressed developmentally down- ...CSA-19 / Large ribosomal subunit protein uL1 / Neural precursor cell expressed developmentally down-regulated protein 6 / NEDD-6


Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62906

+
Protein , 8 types, 8 molecules LmLsSgSfCACDCEi

#41: Protein Ubiquitin-60S ribosomal protein L40 / CEP52 / Ubiquitin A-52 residue ribosomal protein fusion product 1


Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62987
#46: Protein 60S acidic ribosomal protein P0 / 60S ribosomal protein L10E / Large ribosomal subunit protein uL10


Mass: 34309.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05388
#70: 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
#82: 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
#83: Protein Proliferation-associated protein 2G4 / Cell cycle protein p38-2G4 homolog / hG4-1 / ErbB3-binding protein 1


Mass: 43851.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UQ80
#86: Protein Elongation factor 1-alpha 1 / EF-1-alpha-1 / Elongation factor Tu / EF-Tu / Eukaryotic elongation factor 1 A-1 / eEF1A-1 / ...EF-1-alpha-1 / Elongation factor Tu / EF-Tu / Eukaryotic elongation factor 1 A-1 / eEF1A-1 / Leukocyte receptor cluster member 7


Mass: 50214.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68104
#87: Protein Cell growth-regulating nucleolar protein


Mass: 43714.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NX58
#88: 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 natural source
Source: (natural) Severe acute respiratory syndrome coronavirus 2
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

+
40S ribosomal protein ... , 31 types, 31 molecules SASBSDSESFSHSISKSLSPSQSRSSSTSUSVSXSaScSdSCSGSJSMSNSOSWSYSZSbSe

#50: 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
#51: 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
#52: 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
#53: 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
#54: 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
#55: 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
#56: 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
#57: 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
#58: 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
#59: 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
#60: 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
#61: 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
#62: 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
#63: 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
#64: 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
#65: 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
#66: 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
#67: 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
#68: 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
#69: 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
#71: 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
#72: 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
#73: 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
#74: 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
#75: 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
#76: 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
#77: 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
#78: 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
#79: 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
#80: 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
#81: 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

+
Non-polymers , 2 types, 264 molecules

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


Mass: 24.305 Da / Num. of mol.: 256 / Source method: obtained synthetically / Formula: Mg
#90: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 8 / 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 LYAR-80S-eEF1a ribosome complexRIBOSOME#1-#880MULTIPLE SOURCES
2human LYAR-80S-eEF1a ribosome complexCOMPLEX#1-#871NATURAL
3SARS-CoV-2 Nsp1COMPLEX#881NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Severe acute respiratory syndrome coronavirus 22697049
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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11417 / Symmetry type: POINT

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