6ZOK

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

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 SAB [auth A]295Homo sapiensMutation(s): 0 
Gene Names: RPSA, LAMBR, LAMR1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3aC [auth B]264Homo sapiensMutation(s): 0 
Gene Names: RPS3A, FTE1, MFTL
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2D [auth C]293Homo sapiensMutation(s): 0 
Gene Names: RPS2, RPS4
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformE263Homo sapiensMutation(s): 0 
Gene Names: RPS4X, CCG2, RPS4, SCAR
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6F [auth G]249Homo sapiensMutation(s): 0 
Gene Names: RPS6, OK/SW-cl.2
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7G [auth H]194Homo sapiensMutation(s): 0 
Gene Names: RPS7
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8H [auth I]208Homo sapiensMutation(s): 0 
Gene Names: RPS8, OK/SW-cl.83
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9I [auth J]194Homo sapiensMutation(s): 0 
Gene Names: RPS9
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Entity ID: 10
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40S ribosomal protein S11J [auth L]158Homo sapiensMutation(s): 0 
Gene Names: RPS11
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13K [auth N]151Homo sapiensMutation(s): 0 
Gene Names: RPS13
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14L [auth O]151Homo sapiensMutation(s): 0 
Gene Names: RPS14, PRO2640
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Entity ID: 13
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40S ribosomal protein S17M [auth R]135Homo sapiensMutation(s): 0 
Gene Names: RPS17, RPS17L
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Entity ID: 14
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40S ribosomal protein S21N [auth V]83Homo sapiensMutation(s): 0 
Gene Names: RPS21
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Entity ID: 15
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40S ribosomal protein S15aO [auth W]130Homo sapiensMutation(s): 0 
Gene Names: RPS15A, OK/SW-cl.82
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Entity ID: 16
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40S ribosomal protein S23P [auth X]143Homo sapiensMutation(s): 0 
Gene Names: RPS23
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Entity ID: 17
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40S ribosomal protein S24Q [auth Y]130Homo sapiensMutation(s): 0 
Gene Names: RPS24
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26R [auth a]101Homo sapiensMutation(s): 0 
Gene Names: RPS26
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Entity ID: 19
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40S ribosomal protein S27S [auth b]82Homo sapiensMutation(s): 0 
Gene Names: RPS27, MPS1
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Entity ID: 20
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40S ribosomal protein S30T [auth e]56Homo sapiensMutation(s): 0 
Gene Names: FAU
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 1U [auth j]180Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep, 1a-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), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L41V [auth h]25Homo sapiensMutation(s): 0 
Gene Names: RPL41
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S ribosomal RNAA [auth 2]1,869Homo sapiens
Protein Feature View
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
BE [auth a]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
AA [auth 2],
AB [auth 2],
AC [auth 2],
AD [auth 2],
AE [auth X],
AA [auth 2],
AB [auth 2],
AC [auth 2],
AD [auth 2],
AE [auth X],
BA [auth 2],
BB [auth 2],
BC [auth 2],
BD [auth 2],
CA [auth 2],
CB [auth 2],
CC [auth 2],
CD [auth 2],
DA [auth 2],
DB [auth 2],
DC [auth 2],
DD [auth 2],
EA [auth 2],
EB [auth 2],
EC [auth 2],
ED [auth 2],
FA [auth 2],
FB [auth 2],
FC [auth 2],
FD [auth 2],
GA [auth 2],
GB [auth 2],
GC [auth 2],
GD [auth 2],
HA [auth 2],
HB [auth 2],
HC [auth 2],
HD [auth 2],
IA [auth 2],
IB [auth 2],
IC [auth 2],
ID [auth 2],
JA [auth 2],
JB [auth 2],
JC [auth 2],
JD [auth 2],
KA [auth 2],
KB [auth 2],
KC [auth 2],
KD [auth 2],
LA [auth 2],
LB [auth 2],
LC [auth 2],
LD [auth 2],
MA [auth 2],
MB [auth 2],
MC [auth 2],
MD [auth 2],
NA [auth 2],
NB [auth 2],
NC [auth 2],
ND [auth 2],
OA [auth 2],
OB [auth 2],
OC [auth 2],
OD [auth 2],
PA [auth 2],
PB [auth 2],
PC [auth 2],
PD [auth 2],
QA [auth 2],
QB [auth 2],
QC [auth 2],
QD [auth 2],
RA [auth 2],
RB [auth 2],
RC [auth 2],
RD [auth 2],
SA [auth 2],
SB [auth 2],
SC [auth 2],
SD [auth 2],
TA [auth 2],
TB [auth 2],
TC [auth 2],
TD [auth 2],
UA [auth 2],
UB [auth 2],
UC [auth 2],
UD [auth 2],
VA [auth 2],
VB [auth 2],
VC [auth 2],
VD [auth 2],
W [auth 2],
WA [auth 2],
WB [auth 2],
WC [auth 2],
WD [auth 2],
X [auth 2],
XA [auth 2],
XB [auth 2],
XC [auth 2],
XD [auth 2],
Y [auth 2],
YA [auth 2],
YB [auth 2],
YC [auth 2],
YD [auth L],
Z [auth 2],
ZA [auth 2],
ZB [auth 2],
ZC [auth 2],
ZD [auth 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  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references
  • Version 1.2: 2020-10-21
    Changes: Database references
  • Version 1.3: 2021-02-10
    Changes: Database references