7JQC

SARS-CoV-2 Nsp1, CrPV IRES and rabbit 40S ribosome complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA.

Yuan, S.Peng, L.Park, J.J.Hu, Y.Devarkar, S.C.Dong, M.B.Shen, Q.Wu, S.Chen, S.Lomakin, I.B.Xiong, Y.

(2020) Mol Cell 80: 1055-1066.e6

  • DOI: https://doi.org/10.1016/j.molcel.2020.10.034
  • Primary Citation of Related Structures:  
    7JQB, 7JQC

  • PubMed Abstract: 

    The causative virus of the COVID-19 pandemic, SARS-CoV-2, uses its nonstructural protein 1 (Nsp1) to suppress cellular, but not viral, protein synthesis through yet unknown mechanisms. We show here that among all viral proteins, Nsp1 has the largest impact on host viability in the cells of human lung origin. Differential expression analysis of mRNA-seq data revealed that Nsp1 broadly alters the cellular transcriptome. Our cryo-EM structure of the Nsp1-40S ribosome complex shows that Nsp1 inhibits translation by plugging the mRNA entry channel of the 40S. We also determined the structure of the 48S preinitiation complex formed by Nsp1, 40S, and the cricket paralysis virus internal ribosome entry site (IRES) RNA, which shows that it is nonfunctional because of the incorrect position of the mRNA 3' region. Our results elucidate the mechanism of host translation inhibition by SARS-CoV-2 and advance understanding of the impacts from a major pathogenicity factor of SARS-CoV-2.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
eS25B [auth a]125Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAC [auth B]295Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TLT8 (Oryctolagus cuniculus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26D [auth b]115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
eS1E [auth C]264Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
uS5F [auth D]293Oryctolagus cuniculusMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
eS28G [auth d]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S3H [auth E]243Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
eS30I [auth f]133Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uS7J [auth G]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
eS31K [auth g]156Oryctolagus cuniculusMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
eS6L [auth H]249Oryctolagus cuniculusMutation(s): 0 
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Find proteins for A0A5K1UJS7 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
RACK1M [auth h]317Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
eS7N [auth I]194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
eS8O [auth J]208Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
uS4P [auth K]194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
S10_plectin domain-containing proteinQ [auth L]165Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
eS12R [auth N]132Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
uS19S [auth Q]145Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinT [auth R]146Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
eS17U [auth S]135Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
uS13V [auth T]152Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinW [auth U]145Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TN62 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
uS10X [auth V]119Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SIZ2 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21Y [auth W]83Oryctolagus cuniculusMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24130Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Host translation inhibitor nsp1AA [auth F]36Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4CA [auth M]263Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
uS17DA [auth O]158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
uS15EA [auth P]151Oryctolagus cuniculusMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinFA [auth X]168Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
uS8GA [auth Y]130Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinHA [auth c]143Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
eS27IA [auth e]84Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
rRNA1,869Oryctolagus cuniculus
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Entity ID: 28
MoleculeChains LengthOrganismImage
Cricket paralysis virus IRES RNABA [auth i]192Cricket paralysis virus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references
  • Version 1.2: 2021-01-27
    Changes: Structure summary
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references