7K5I

SARS-COV-2 nsp1 in complex with human 40S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

SARS-CoV-2 Nsp1 suppresses host but not viral translation through a bipartite mechanism.

Shi, M.Wang, L.Fontana, P.Vora, S.Zhang, Y.Fu, T.M.Lieberman, J.Wu, H.

(2020) Biorxiv 

  • DOI: 10.1101/2020.09.18.302901
  • Primary Citation of Related Structures:  
    7K5I

  • PubMed Abstract: 
  • The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a highly contagious virus that underlies the current COVID-19 pandemic. SARS-CoV-2 is thought to disable various features of host immunity and cellular defense. The SARS-CoV-2 nonstructural protein 1 (Nsp1) is known to inhibit host protein translation and could be a target for antiviral therapy against COVID-19 ...

    The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a highly contagious virus that underlies the current COVID-19 pandemic. SARS-CoV-2 is thought to disable various features of host immunity and cellular defense. The SARS-CoV-2 nonstructural protein 1 (Nsp1) is known to inhibit host protein translation and could be a target for antiviral therapy against COVID-19. However, how SARS-CoV-2 circumvents this translational blockage for the production of its own proteins is an open question. Here, we report a bipartite mechanism of SARS-CoV-2 Nsp1 which operates by: (1) hijacking the host ribosome via direct interaction of its C-terminal domain (CT) with the 40S ribosomal subunit and (2) specifically lifting this inhibition for SARS-CoV-2 via a direct interaction of its N-terminal domain (NT) with the 5' untranslated region (5' UTR) of SARS-CoV-2 mRNA. We show that while Nsp1-CT is sufficient for binding to 40S and inhibition of host protein translation, the 5' UTR of SARS-CoV-2 mRNA removes this inhibition by binding to Nsp1-NT, suggesting that the Nsp1-NT-UTR interaction is incompatible with the Nsp1-CT-40S interaction. Indeed, lengthening the linker between Nsp1-NT and Nsp1-CT of Nsp1 progressively reduced the ability of SARS-CoV-2 5' UTR to escape the translational inhibition, supporting that the incompatibility is likely steric in nature. The short SL1 region of the 5' UTR is required for viral mRNA translation in the presence of Nsp1. Thus, our data provide a comprehensive view on how Nsp1 switches infected cells from host mRNA translation to SARS-CoV-2 mRNA translation, and that Nsp1 and 5' UTR may be targeted for anti-COVID-19 therapeutics.


    Organizational Affiliation

    Lilly Research Laboratories, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, Indiana 46285.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17A [auth R]135Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S29C [auth d]56Homo sapiensMutation(s): 0 
Gene Names: RPS29
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3D243Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5E [auth F]204Homo sapiensMutation(s): 0 
Gene Names: RPS5
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10F [auth K]165Homo sapiensMutation(s): 0 
Gene Names: RPS10
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12G [auth M]132Homo sapiensMutation(s): 0 
Gene Names: RPS12
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Entity ID: 8
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40S ribosomal protein S15H [auth P]145Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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Entity ID: 9
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40S ribosomal protein S16I [auth Q]146Homo sapiensMutation(s): 0 
Gene Names: RPS16
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Entity ID: 10
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40S ribosomal protein S18J [auth S]152Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19K [auth T]145Homo sapiensMutation(s): 0 
Gene Names: RPS19
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Entity ID: 12
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40S ribosomal protein S20L [auth U]119Homo sapiensMutation(s): 0 
Gene Names: RPS20
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Entity ID: 13
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40S ribosomal protein S25M [auth Z]125Homo sapiensMutation(s): 0 
Gene Names: RPS25
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28N [auth c]69Homo sapiensMutation(s): 0 
Gene Names: RPS28
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Entity ID: 15
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40S ribosomal protein S27aO [auth f]149Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1P [auth g]317Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
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Entity ID: 17
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40S ribosomal protein SAQ [auth A]295Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
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Entity ID: 18
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40S ribosomal protein S3aR [auth B]264Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
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Entity ID: 19
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40S ribosomal protein S2S [auth C]293Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
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Entity ID: 20
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40S ribosomal protein S4, X isoformT [auth E]263Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
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Entity ID: 21
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40S ribosomal protein S6U [auth G]249Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
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Entity ID: 22
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40S ribosomal protein S7V [auth H]194Homo sapiensMutation(s): 0 
Gene Names: RPS7
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Entity ID: 23
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40S ribosomal protein S8W [auth I]208Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
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Entity ID: 24
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40S ribosomal protein S9X [auth J]194Homo sapiensMutation(s): 0 
Gene Names: RPS9
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Entity ID: 25
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40S ribosomal protein S11Y [auth L]158Homo sapiensMutation(s): 0 
Gene Names: RPS11
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13Z [auth N]151Homo sapiensMutation(s): 0 
Gene Names: RPS13
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14AA [auth O]151Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
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Entity ID: 28
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40S ribosomal protein S21BA [auth V]83Homo sapiensMutation(s): 0 
Gene Names: RPS21
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15aCA [auth W]130Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23DA [auth X]143Homo sapiensMutation(s): 0 
Gene Names: RPS23
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Entity ID: 31
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40S ribosomal protein S24EA [auth Y]133Homo sapiensMutation(s): 0 
Gene Names: RPS24
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26FA [auth a]102Homo sapiensMutation(s): 0 
Gene Names: RPS26
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Entity ID: 33
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40S ribosomal protein S27GA [auth b]84Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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Entity ID: 34
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40S ribosomal protein S30HA [auth e]59Homo sapiensMutation(s): 0 
Gene Names: FAU
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Entity ID: 35
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60S ribosomal protein L41IA [auth h]25Homo sapiensMutation(s): 0 
Gene Names: RPL41
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Host translation inhibitor nsp1JA [auth 1]180Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
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Entity ID: 2
MoleculeChainsLengthOrganismImage
40S ribosomal rRNA18SB [auth 2]1868Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
LA [auth d], MA [auth f], NA [auth a]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
KA [auth 2]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2020-09-16 
  • Released Date: 2020-10-14 
  • Deposition Author(s): Wang, L., Shi, M., Wu, H.

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Structure summary
  • Version 2.0: 2021-03-17
    Type: Coordinate replacement
    Reason: Atomic clashes
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Source and taxonomy, Structure summary