6ZON

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.

Thoms, M.Buschauer, R.Ameismeier, M.Koepke, L.Denk, T.Hirschenberger, M.Kratzat, H.Hayn, M.Mackens-Kiani, T.Cheng, J.Straub, J.H.Sturzel, C.M.Frohlich, T.Berninghausen, O.Becker, T.Kirchhoff, F.Sparrer, K.M.J.Beckmann, R.

(2020) Science 369: 1249-1255

  • DOI: https://doi.org/10.1126/science.abc8665
  • Primary Citation of Related Structures:  
    6ZLW, 6ZM7, 6ZME, 6ZMI, 6ZMO, 6ZMT, 6ZN5, 6ZON, 6ZP4

  • PubMed 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 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 S 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 S and various native Nsp1-40 S and -80 S 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.


  • Organizational Affiliation

    Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAA [auth a]295Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aB [auth p]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2C [auth d]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26D [auth Q]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197728 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformE [auth q]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41F [auth W]25Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6G [auth r]249Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7H [auth s]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8I [auth t]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9J [auth c]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11K [auth n]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13L [auth m]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14M [auth i]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21N [auth y]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aO [auth f]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23P [auth j]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24Q [auth z]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2784Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30S [auth T]59Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17U [auth w]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16V [auth g]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3W [auth b]243Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5X [auth e]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10Y [auth u]165Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12Z [auth v]132Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15AA [auth o]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18BA [auth k]152Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19CA [auth x]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20DA [auth h]119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008988 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25EA [auth P]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28FA [auth S]69Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29GA [auth l]56Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aHA [auth U]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1IA [auth V]317Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204628 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit IJA [auth I]325Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000084623 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit BKA [auth B]814Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106263 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit A,Eukaryotic translation initiation factor 3 subunit ALA [auth A]703Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000107581 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit CMA [auth C]913Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000184110 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit ENA [auth E]445Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000104408 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit FOA [auth F]357Homo sapiensMutation(s): 0 
EC: 3.4.19.12
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GTEx:  ENSG00000175390 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit HPA [auth H]352Homo sapiensMutation(s): 0 
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Find proteins for O15372 (Homo sapiens)
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PHAROS:  O15372
GTEx:  ENSG00000147677 
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UniProt GroupO15372
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit KQA [auth K]218Homo sapiensMutation(s): 0 
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PHAROS:  Q9UBQ5
GTEx:  ENSG00000178982 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit LRA [auth L]564Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100129 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit MSA [auth M]374Homo sapiensMutation(s): 0 
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PHAROS:  Q7L2H7
GTEx:  ENSG00000149100 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit DTA [auth D]548Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100353 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown factorUA [auth Y]78Homo sapiensMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Host translation inhibitor Nsp1VA [auth J]180Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data), 2.1.1 (PDB Primary Data)
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Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
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Entity ID: 20
MoleculeChains LengthOrganismImage
18S ribosomal RNAT [auth 2]1,868Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB/TRR-174
German Research Foundation (DFG)GermanyBE1814/15-1
German Research Foundation (DFG)GermanyBE1814/1-1

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references