6ZOJ

SARS-CoV-2-Nsp1-40S complex, composite map


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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

SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation.

Schubert, K.Karousis, E.D.Jomaa, A.Scaiola, A.Echeverria, B.Gurzeler, L.A.Leibundgut, M.Thiel, V.Muhlemann, O.Ban, N.

(2020) Nat Struct Mol Biol 27: 959-966

  • DOI: 10.1038/s41594-020-0511-8
  • Primary Citation of Related Structures:  
    6ZOJ, 6ZOL, 6ZOK

  • PubMed Abstract: 
  • The SARS-CoV-2 non-structural protein 1 (Nsp1), also referred to as the host shutoff factor, suppresses host innate immune functions. By combining cryo-electron microscopy and biochemistry, we show that SARS-CoV-2 Nsp1 binds to the human 40S subunit ...

    The SARS-CoV-2 non-structural protein 1 (Nsp1), also referred to as the host shutoff factor, suppresses host innate immune functions. By combining cryo-electron microscopy and biochemistry, we show that SARS-CoV-2 Nsp1 binds to the human 40S subunit in ribosomal complexes, including the 43S pre-initiation complex and the non-translating 80S ribosome. The protein inserts its C-terminal domain into the mRNA channel, where it interferes with mRNA binding. We observe translation inhibition in the presence of Nsp1 in an in vitro translation system and in human cells. Based on the high-resolution structure of the 40S-Nsp1 complex, we identify residues of Nsp1 crucial for mediating translation inhibition. We further show that the full-length 5' untranslated region of the genomic viral mRNA stimulates translation in vitro, suggesting that SARS-CoV-2 combines global inhibition of translation by Nsp1 with efficient translation of the viral mRNA to allow expression of viral genes.


    Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland. ban@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein SAA295Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
Find proteins for P08865 (Homo sapiens)
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PHAROS  P08865
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3aB264Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
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PHAROS  P61247
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2C293Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
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PHAROS  P15880
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3D243Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
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PHAROS  P23396
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformE263Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
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PHAROS  P62701
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5F204Homo sapiensMutation(s): 0 
Gene Names: RPS5
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PHAROS  P46782
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6G249Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
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PHAROS  P62753
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7H194Homo sapiensMutation(s): 0 
Gene Names: RPS7
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PHAROS  P62081
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8I208Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
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PHAROS  P62241
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9J194Homo sapiensMutation(s): 0 
Gene Names: RPS9
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10K165Homo sapiensMutation(s): 0 
Gene Names: RPS10
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PHAROS  P46783
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11L158Homo sapiensMutation(s): 0 
Gene Names: RPS11
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12M132Homo sapiensMutation(s): 0 
Gene Names: RPS12
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PHAROS  P25398
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Entity ID: 15
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40S ribosomal protein S13N151Homo sapiensMutation(s): 0 
Gene Names: RPS13
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14O151Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
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Entity ID: 17
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40S ribosomal protein S15P145Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16Q146Homo sapiensMutation(s): 0 
Gene Names: RPS16
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Entity ID: 19
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40S ribosomal protein S17R135Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
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PHAROS  P08708
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Entity ID: 20
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40S ribosomal protein S18S152Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19T145Homo sapiensMutation(s): 0 
Gene Names: RPS19
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PHAROS  P39019
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Entity ID: 22
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40S ribosomal protein S20U119Homo sapiensMutation(s): 0 
Gene Names: RPS20
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PHAROS  P60866
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21V83Homo sapiensMutation(s): 0 
Gene Names: RPS21
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PHAROS  P63220
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15aW130Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23X143Homo sapiensMutation(s): 0 
Gene Names: RPS23
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24Y130Homo sapiensMutation(s): 0 
Gene Names: RPS24
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25Z125Homo sapiensMutation(s): 0 
Gene Names: RPS25
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26a101Homo sapiensMutation(s): 0 
Gene Names: RPS26
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27b82Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28c61Homo sapiensMutation(s): 0 
Gene Names: RPS28
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S29d55Homo sapiensMutation(s): 0 
Gene Names: RPS29
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30e56Homo sapiensMutation(s): 0 
Gene Names: FAU
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Entity ID: 33
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Ribosomal protein S27af72Homo sapiensMutation(s): 0 
Gene Names: RPS27A
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1g315Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 1j180Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
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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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L41h25Homo sapiensMutation(s): 0 
Gene Names: RPL41
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S ribosomal RNA21869Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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a, d, f
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
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2, G, O, S, T, X
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland173085
Swiss National Science FoundationSwitzerland182341
Swiss National Science FoundationSwitzerland182831

Revision History 

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references, Derived calculations
  • Version 1.2: 2020-10-21
    Changes: Database references