9NPX | pdb_00009npx

SARS-CoV-2 nsp1 bound to the Rhinolophus lepidus 40S ribosomal subunit (local refinement of the 40S body)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 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

SARS-CoV-2 nsp1 mediates broad inhibition of translation in mammals.

Gen, R.Addetia, A.Asarnow, D.Park, Y.J.Quispe, J.Chan, M.C.Brown, J.T.Lee, J.Campbell, M.G.Lapointe, C.P.Veesler, D.

(2025) Cell Rep 44: 115696-115696

  • DOI: https://doi.org/10.1016/j.celrep.2025.115696
  • Primary Citation of Related Structures:  
    9NPX, 9NPY

  • PubMed Abstract: 

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) non-structural protein 1 (nsp1) promotes innate immune evasion by inhibiting host translation in human cells. However, the role of nsp1 in other host species remains elusive, especially in bats-natural reservoirs of sarbecoviruses with a markedly different innate immune system than humans. We reveal that nsp1 potently inhibits translation in Rhinolophus lepidus bat cells, which belong to the same genus as known sarbecovirus reservoir hosts. We determined a cryoelectron microscopy structure of nsp1 bound to the R. lepidus 40S ribosomal subunit, showing that it blocks the mRNA entry channel by targeting a highly conserved site among mammals. Accordingly, we found that nsp1 blocked protein translation in mammalian cells from several species, underscoring its broadly inhibitory activity and conserved role in numerous SARS-CoV-2 hosts. Our findings illuminate the arms race between coronaviruses and mammalian host immunity, providing a foundation for understanding the determinants of viral maintenance in bat hosts and spillover.


  • Organizational Affiliation
    • Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2293Rhinolophus lepidusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformB [auth D]263Rhinolophus lepidusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6C [auth F]249Rhinolophus lepidusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8D [auth H]208Rhinolophus lepidusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9E [auth I]194Rhinolophus lepidusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13F [auth M]151Rhinolophus lepidusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14G [auth N]151Rhinolophus lepidusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aH [auth P]130Rhinolophus lepidusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17I [auth R]135Rhinolophus lepidusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21J [auth V]84Rhinolophus lepidusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23K [auth W]143Rhinolophus lepidusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24L [auth X]130Rhinolophus lepidusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26M [auth Z]115Rhinolophus lepidusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27N [auth a]84Rhinolophus lepidusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41O [auth f]25Rhinolophus lepidusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAP [auth h]295Rhinolophus lepidusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Host translation inhibitor nsp1Q [auth j]180Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
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Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 1R [auth k]113Homo sapiensMutation(s): 0 
Gene Names: EIF1SUI1
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Find proteins for P41567 (Homo sapiens)
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PHAROS:  P41567
GTEx:  ENSG00000173812 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7S [auth G]194Rhinolophus lepidusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11T [auth K]158Rhinolophus lepidusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30U [auth e]61Rhinolophus lepidusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aV [auth C]264Rhinolophus lepidusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS3, RPS3X [auth B]243Rhinolophus lepidusMutation(s): 0 
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Entity ID: 23
MoleculeChains LengthOrganismImage
18S ribosomal RNAW [auth i]1,869Rhinolophus lepidus
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth Z]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
AA [auth Z]
GC [auth i]
HC [auth i]
IC [auth i]
JC [auth i]
AA [auth Z],
GC [auth i],
HC [auth i],
IC [auth i],
JC [auth i],
KC [auth i],
LC [auth i],
MC [auth i],
NC [auth i],
OC [auth i],
PC [auth i],
QC [auth i],
Z [auth N]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth i]
AC [auth i]
BB [auth i]
BC [auth i]
CA [auth i]
AB [auth i],
AC [auth i],
BB [auth i],
BC [auth i],
CA [auth i],
CB [auth i],
CC [auth i],
DA [auth i],
DB [auth i],
DC [auth i],
EA [auth i],
EB [auth i],
EC [auth i],
FA [auth i],
FB [auth i],
FC [auth i],
GA [auth i],
GB [auth i],
HA [auth i],
HB [auth i],
IA [auth i],
IB [auth i],
JA [auth i],
JB [auth i],
KA [auth i],
KB [auth i],
LA [auth i],
LB [auth i],
MA [auth i],
MB [auth i],
NA [auth i],
NB [auth i],
OA [auth i],
OB [auth i],
PA [auth i],
PB [auth i],
QA [auth i],
QB [auth i],
RA [auth i],
RB [auth i],
SA [auth i],
SB [auth i],
TA [auth i],
TB [auth i],
UA [auth i],
UB [auth i],
VA [auth i],
VB [auth i],
WA [auth i],
WB [auth i],
XA [auth i],
XB [auth i],
Y [auth F],
YA [auth i],
YB [auth i],
ZA [auth i],
ZB [auth i]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-07-30
    Changes: Data collection, Other, Structure summary