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 1.3 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: RPSALAMBRLAMR1
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GTEx:  ENSG00000168028 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3aC [auth B]264Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
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GTEx:  ENSG00000145425 
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Entity ID: 4
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40S ribosomal protein S2D [auth C]293Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
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GTEx:  ENSG00000140988 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3E [auth D]243Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 6
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40S ribosomal protein S4, X isoformF [auth E]263Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
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Entity ID: 7
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40S ribosomal protein S5G [auth F]204Homo sapiensMutation(s): 0 
Gene Names: RPS5
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GTEx:  ENSG00000083845 
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Entity ID: 8
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40S ribosomal protein S6H [auth G]249Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
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GTEx:  ENSG00000137154 
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Entity ID: 9
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40S ribosomal protein S7I [auth H]194Homo sapiensMutation(s): 0 
Gene Names: RPS7
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GTEx:  ENSG00000171863 
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Entity ID: 10
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40S ribosomal protein S8J [auth I]208Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
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GTEx:  ENSG00000142937 
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Entity ID: 11
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40S ribosomal protein S9K [auth J]194Homo sapiensMutation(s): 0 
Gene Names: RPS9
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GTEx:  ENSG00000170889 
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Entity ID: 12
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40S ribosomal protein S10L [auth K]165Homo sapiensMutation(s): 0 
Gene Names: RPS10
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Entity ID: 13
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40S ribosomal protein S11M [auth L]158Homo sapiensMutation(s): 0 
Gene Names: RPS11
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40S ribosomal protein S12N [auth M]132Homo sapiensMutation(s): 0 
Gene Names: RPS12
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GTEx:  ENSG00000112306 
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Entity ID: 15
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40S ribosomal protein S13O [auth N]151Homo sapiensMutation(s): 0 
Gene Names: RPS13
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GTEx:  ENSG00000110700 
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Entity ID: 16
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40S ribosomal protein S14P [auth O]151Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
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Entity ID: 17
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40S ribosomal protein S15Q [auth P]145Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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GTEx:  ENSG00000115268 
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Entity ID: 18
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40S ribosomal protein S16R [auth Q]146Homo sapiensMutation(s): 0 
Gene Names: RPS16
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GTEx:  ENSG00000105193 
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Entity ID: 19
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40S ribosomal protein S17S [auth R]135Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
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GTEx:  ENSG00000182774 
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Entity ID: 20
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40S ribosomal protein S18T [auth S]152Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
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GTEx:  ENSG00000231500 
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Entity ID: 21
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40S ribosomal protein S19U [auth T]145Homo sapiensMutation(s): 0 
Gene Names: RPS19
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GTEx:  ENSG00000105372 
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Entity ID: 22
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40S ribosomal protein S20V [auth U]119Homo sapiensMutation(s): 0 
Gene Names: RPS20
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GTEx:  ENSG00000008988 
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Entity ID: 23
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40S ribosomal protein S21W [auth V]83Homo sapiensMutation(s): 0 
Gene Names: RPS21
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GTEx:  ENSG00000171858 
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Entity ID: 24
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40S ribosomal protein S15aX [auth W]130Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
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GTEx:  ENSG00000134419 
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Entity ID: 25
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40S ribosomal protein S23Y [auth X]143Homo sapiensMutation(s): 0 
Gene Names: RPS23
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GTEx:  ENSG00000186468 
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Entity ID: 26
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40S ribosomal protein S24Z [auth Y]130Homo sapiensMutation(s): 0 
Gene Names: RPS24
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Entity ID: 27
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40S ribosomal protein S25AA [auth Z]125Homo sapiensMutation(s): 0 
Gene Names: RPS25
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GTEx:  ENSG00000118181 
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Entity ID: 28
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40S ribosomal protein S26BA [auth a]101Homo sapiensMutation(s): 0 
Gene Names: RPS26
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GTEx:  ENSG00000197728 
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Entity ID: 29
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40S ribosomal protein S27CA [auth b]82Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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GTEx:  ENSG00000177954 
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Entity ID: 30
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40S ribosomal protein S28DA [auth c]61Homo sapiensMutation(s): 0 
Gene Names: RPS28
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GTEx:  ENSG00000233927 
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40S ribosomal protein S29EA [auth d]55Homo sapiensMutation(s): 0 
Gene Names: RPS29
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GTEx:  ENSG00000213741 
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Entity ID: 32
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40S ribosomal protein S30FA [auth e]56Homo sapiensMutation(s): 0 
Gene Names: FAU
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Entity ID: 33
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Ribosomal protein S27aGA [auth f]72Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
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GTEx:  ENSG00000143947 
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Entity ID: 34
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Receptor of activated protein C kinase 1HA [auth g]315Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
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GTEx:  ENSG00000204628 
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Entity ID: 35
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Non-structural protein 1IA [auth j]180Severe 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), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L41JA [auth h]25Homo sapiensMutation(s): 0 
Gene Names: RPL41
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GTEx:  ENSG00000229117 
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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 
UG [auth a],
VG [auth d],
WG [auth f]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 2],
AC [auth 2],
AD [auth 2],
AE [auth 2],
AF [auth 2],
AB [auth 2],
AC [auth 2],
AD [auth 2],
AE [auth 2],
AF [auth 2],
AG [auth 2],
BB [auth 2],
BC [auth 2],
BD [auth 2],
BE [auth 2],
BF [auth 2],
BG [auth 2],
CB [auth 2],
CC [auth 2],
CD [auth 2],
CE [auth 2],
CF [auth 2],
CG [auth 2],
DB [auth 2],
DC [auth 2],
DD [auth 2],
DE [auth 2],
DF [auth 2],
DG [auth 2],
EB [auth 2],
EC [auth 2],
ED [auth 2],
EE [auth 2],
EF [auth 2],
EG [auth 2],
FB [auth 2],
FC [auth 2],
FD [auth 2],
FE [auth 2],
FF [auth 2],
FG [auth 2],
GB [auth 2],
GC [auth 2],
GD [auth 2],
GE [auth 2],
GF [auth 2],
GG [auth 2],
HB [auth 2],
HC [auth 2],
HD [auth 2],
HE [auth 2],
HF [auth 2],
HG [auth 2],
IB [auth 2],
IC [auth 2],
ID [auth 2],
IE [auth 2],
IF [auth 2],
IG [auth 2],
JB [auth 2],
JC [auth 2],
JD [auth 2],
JE [auth 2],
JF [auth 2],
JG [auth 2],
KA [auth 2],
KB [auth 2],
KC [auth 2],
KD [auth 2],
KE [auth 2],
KF [auth 2],
KG [auth 2],
LA [auth 2],
LB [auth 2],
LC [auth 2],
LD [auth 2],
LE [auth 2],
LF [auth 2],
LG [auth 2],
MA [auth 2],
MB [auth 2],
MC [auth 2],
MD [auth 2],
ME [auth 2],
MF [auth 2],
MG [auth 2],
NA [auth 2],
NB [auth 2],
NC [auth 2],
ND [auth 2],
NE [auth 2],
NF [auth 2],
NG [auth G],
OA [auth 2],
OB [auth 2],
OC [auth 2],
OD [auth 2],
OE [auth 2],
OF [auth 2],
OG [auth O],
PA [auth 2],
PB [auth 2],
PC [auth 2],
PD [auth 2],
PE [auth 2],
PF [auth 2],
PG [auth O],
QA [auth 2],
QB [auth 2],
QC [auth 2],
QD [auth 2],
QE [auth 2],
QF [auth 2],
QG [auth S],
RA [auth 2],
RB [auth 2],
RC [auth 2],
RD [auth 2],
RE [auth 2],
RF [auth 2],
RG [auth S],
SA [auth 2],
SB [auth 2],
SC [auth 2],
SD [auth 2],
SE [auth 2],
SF [auth 2],
SG [auth T],
TA [auth 2],
TB [auth 2],
TC [auth 2],
TD [auth 2],
TE [auth 2],
TF [auth 2],
TG [auth X],
UA [auth 2],
UB [auth 2],
UC [auth 2],
UD [auth 2],
UE [auth 2],
UF [auth 2],
VA [auth 2],
VB [auth 2],
VC [auth 2],
VD [auth 2],
VE [auth 2],
VF [auth 2],
WA [auth 2],
WB [auth 2],
WC [auth 2],
WD [auth 2],
WE [auth 2],
WF [auth 2],
XA [auth 2],
XB [auth 2],
XC [auth 2],
XD [auth 2],
XE [auth 2],
XF [auth 2],
YA [auth 2],
YB [auth 2],
YC [auth 2],
YD [auth 2],
YE [auth 2],
YF [auth 2],
ZA [auth 2],
ZB [auth 2],
ZC [auth 2],
ZD [auth 2],
ZE [auth 2],
ZF [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