6ZOL

SARS-CoV-2-Nsp1-40S complex, focused on head


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 1.3 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, 6ZOK, 6ZOL

  • 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 in ribosomal complexes, including the 43S pre-initiation complex and the non-translating 80S ribosome ...

    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 S3B [auth D]243Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
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PHAROS:  P23396
GTEx:  ENSG00000149273 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5C [auth F]204Homo sapiensMutation(s): 0 
Gene Names: RPS5
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PHAROS:  P46782
GTEx:  ENSG00000083845 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10D [auth K]165Homo sapiensMutation(s): 0 
Gene Names: RPS10
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12E [auth M]132Homo sapiensMutation(s): 0 
Gene Names: RPS12
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GTEx:  ENSG00000112306 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15F [auth P]145Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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GTEx:  ENSG00000115268 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16G [auth Q]146Homo sapiensMutation(s): 0 
Gene Names: RPS16
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GTEx:  ENSG00000105193 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17H [auth R]135Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
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GTEx:  ENSG00000182774 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18I [auth S]152Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
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GTEx:  ENSG00000231500 
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Entity ID: 10
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40S ribosomal protein S19J [auth T]145Homo sapiensMutation(s): 0 
Gene Names: RPS19
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GTEx:  ENSG00000105372 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S20K [auth U]119Homo sapiensMutation(s): 0 
Gene Names: RPS20
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GTEx:  ENSG00000008988 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25L [auth Z]125Homo sapiensMutation(s): 0 
Gene Names: RPS25
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GTEx:  ENSG00000118181 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28M [auth c]61Homo sapiensMutation(s): 0 
Gene Names: RPS28
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GTEx:  ENSG00000233927 
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Entity ID: 14
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40S ribosomal protein S29N [auth d]55Homo sapiensMutation(s): 0 
Gene Names: RPS29
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GTEx:  ENSG00000213741 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S27aO [auth f]72Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
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GTEx:  ENSG00000143947 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1P [auth g]315Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
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GTEx:  ENSG00000204628 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S ribosomal RNAA [auth 2]1869Homo 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 
VB [auth d],
WB [auth f]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth 2],
AB [auth 2],
BA [auth 2],
BB [auth 2],
CA [auth 2],
AA [auth 2],
AB [auth 2],
BA [auth 2],
BB [auth 2],
CA [auth 2],
CB [auth 2],
DA [auth 2],
DB [auth 2],
EA [auth 2],
EB [auth 2],
FA [auth 2],
FB [auth 2],
GA [auth 2],
GB [auth 2],
HA [auth 2],
HB [auth 2],
IA [auth 2],
IB [auth 2],
JA [auth 2],
JB [auth 2],
KA [auth 2],
KB [auth 2],
LA [auth 2],
LB [auth 2],
MA [auth 2],
MB [auth 2],
NA [auth 2],
NB [auth 2],
OA [auth 2],
OB [auth 2],
PA [auth 2],
PB [auth 2],
Q [auth 2],
QA [auth 2],
QB [auth 2],
R [auth 2],
RA [auth 2],
RB [auth F],
S [auth 2],
SA [auth 2],
SB [auth S],
T [auth 2],
TA [auth 2],
TB [auth S],
U [auth 2],
UA [auth 2],
UB [auth T],
V [auth 2],
VA [auth 2],
W [auth 2],
WA [auth 2],
X [auth 2],
XA [auth 2],
Y [auth 2],
YA [auth 2],
Z [auth 2],
ZA [auth 2]
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

View Full Validation Report




Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2021-02-10
    Changes: Database references