[English] 日本語
EMN Papers
- Database of articles cited by 3DEM data entries -

+
Search query

Keywords
Author
Journal
IF

-
Structure paper

TitleStructural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Journal, issue, pagesScience, Year 2020
Publish dateJul 17, 2020
AuthorsMatthias 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 /
PubMed AbstractSARS-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.
External linksPubMed:32680882 / Publisher's page
KeywordsVIRAL PROTEIN / Translational Inhibition / SARS-CoV-2 / Immune Evasion / Human Ribosome
MethodsEM (single particle)
Resolution2.6 - 3.2 A
Structure data

EMDB-11276:
SARS-CoV-2 Nsp1 bound to the human 40S ribosomal subunit

EMDB-11288:
SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex

EMDB-11289:
SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-eERF1 ribosome complex

EMDB-11310:
SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex - state 2

EMDB-11325:
SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1

EMDB-11335:
SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2

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

PDB-6zm7:
SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex

PDB-6zme:
SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-eERF1 ribosome complex

PDB-6zn5:
SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex - state 2

PDB-6zon:
SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1

PDB-6zp4:
SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2

Chemicals

ChemComp-ZN:
ZINC ION / Zinc

ChemComp-MG:
MAGNESIUM ION / Magnesium

ChemComp-SF4:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

Source
  • homo sapiens (human)
  • severe acute respiratory syndrome coronavirus 2
  • Human (human)
  • 2019-nCoV (virus)

+
About EMN Papers

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jul 5, 2019. Downlodablable text data

Downlodablable text data

  • Some data of EM Navigator services can be downloaded as text file. Software such as Excel can load the data files.
    PageDataFormat
    EMN Searchsearch resultCSV, TSV, or JSON
    EMN statisticsdata tableCSV or TSV

Related info.:EMN Search / EMN Statistics

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Feb 20, 2018. PDBj/BINDS workshop in Osaka University

PDBj/BINDS workshop in Osaka University

    Read more

    -
    EMN Papers

    Database of articles cited by 3DEM data entries

    • Database of articles cited by 3DEM data entries in EMDB and PDB
    • Using PubMed data

    Related info.:EMDB / PDB / Q: What is the data source of EM Navigator? / EM Navigator / Yorodumi Papers / Changes in new EM Navigator and Yorodumi

    Read more