8T4S

MERS-CoV Nsp1 protein bound to the Human 40S Ribosomal subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for translation inhibition by MERS-CoV Nsp1 reveals a conserved mechanism for betacoronaviruses.

Devarkar, S.C.Vetick, M.Balaji, S.Lomakin, I.B.Yang, L.Jin, D.Gilbert, W.V.Chen, S.Xiong, Y.

(2023) Cell Rep 42: 113156-113156

  • DOI: https://doi.org/10.1016/j.celrep.2023.113156
  • Primary Citation of Related Structures:  
    8T4S

  • PubMed Abstract: 

    All betacoronaviruses (β-CoVs) encode non-structural protein 1 (Nsp1), an essential pathogenicity factor that potently restricts host gene expression. Among the β-CoV family, MERS-CoV is the most distantly related member to SARS-CoV-2, and the mechanism for host translation inhibition by MERS-CoV Nsp1 remains controversial. Herein, we show that MERS-CoV Nsp1 directly interacts with the 40S ribosomal subunit. Using cryogenic electron microscopy (cryo-EM), we report a 2.6-Å structure of the MERS-CoV Nsp1 bound to the human 40S ribosomal subunit. The extensive interactions between C-terminal domain of MERS-CoV Nsp1 and the mRNA entry channel of the 40S ribosomal subunit are critical for its translation inhibition function. This mechanism of MERS-CoV Nsp1 is strikingly similar to SARS-CoV and SARS-CoV-2 Nsp1, despite modest sequence conservation. Our results reveal that the mechanism of host translation inhibition is conserved across β-CoVs and highlight a potential therapeutic target for the development of antivirals that broadly restrict β-CoVs.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAB [auth A]295Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aC [auth B]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2D [auth C]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3E [auth D]243Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformF [auth E]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5G [auth F]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6H [auth G]249Homo sapiensMutation(s): 1 
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GTEx:  ENSG00000137154 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7I [auth H]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8J [auth I]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9K [auth J]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10L [auth K]165Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11M [auth L]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12N [auth M]132Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13O [auth N]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14P [auth O]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15Q [auth P]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16R [auth Q]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17S [auth R]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18T [auth S]152Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19U [auth T]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20V [auth U]119Homo sapiensMutation(s): 0 
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Find proteins for P60866 (Homo sapiens)
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GTEx:  ENSG00000008988 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21W [auth V]83Homo sapiensMutation(s): 0 
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Find proteins for P63220 (Homo sapiens)
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GTEx:  ENSG00000171858 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aX [auth W]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23Y [auth X]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24Z [auth Y]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25AA [auth Z]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26BA [auth a]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197728 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27CA [auth b]84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28DA [auth c]69Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29EA [auth d]56Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
FAU ubiquitin-like and ribosomal protein S30FA [auth e]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aGA [auth f]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1HA [auth g]317Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204628 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41IA [auth h]25Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Replicase polyprotein 1abJA [auth n]193Middle East respiratory syndrome-related coronavirusMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S rRNAA [auth 2]1,869Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
DE [auth a],
EE [auth d],
FE [auth f]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 2]
AC [auth 2]
AD [auth 2]
AE [auth 2]
BB [auth 2]
AB [auth 2],
AC [auth 2],
AD [auth 2],
AE [auth 2],
BB [auth 2],
BC [auth 2],
BD [auth 2],
BE [auth 2],
CB [auth 2],
CC [auth 2],
CD [auth 2],
CE [auth I],
DB [auth 2],
DC [auth 2],
DD [auth 2],
EB [auth 2],
EC [auth 2],
ED [auth 2],
FB [auth 2],
FC [auth 2],
FD [auth 2],
GB [auth 2],
GC [auth 2],
GD [auth 2],
HB [auth 2],
HC [auth 2],
HD [auth 2],
IB [auth 2],
IC [auth 2],
ID [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],
WA [auth 2],
WB [auth 2],
WC [auth 2],
WD [auth 2],
XA [auth 2],
XB [auth 2],
XC [auth 2],
XD [auth 2],
YA [auth 2],
YB [auth 2],
YC [auth 2],
YD [auth 2],
ZA [auth 2],
ZB [auth 2],
ZC [auth 2],
ZD [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Database references