9NPY image
Deposition Date 2025-03-11
Release Date 2025-06-11
Last Version Date 2025-06-11
Entry Detail
PDB ID:
9NPY
Keywords:
Title:
SARS-CoV-2 nsp1 bound to the Rhinolophus lepidus 40S ribosome (local refinement of the 40S head)
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS3, RPS3
Chain IDs:A (auth: B)
Chain Length:156
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS7, RPS5
Chain IDs:O (auth: E)
Chain Length:204
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS10, RPS10
Chain IDs:B (auth: J)
Chain Length:165
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS12, RPS12
Chain IDs:C (auth: L)
Chain Length:132
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS19, RPS15
Chain IDs:D (auth: O)
Chain Length:145
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS9, RPS16
Chain IDs:E (auth: Q)
Chain Length:146
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS17, RPS17
Chain IDs:F (auth: R)
Chain Length:135
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS13, RPS18
Chain IDs:G (auth: S)
Chain Length:152
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS19, RPS19
Chain IDs:H (auth: T)
Chain Length:145
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS10, RPS20
Chain IDs:I (auth: U)
Chain Length:119
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS25, RPS25
Chain IDs:J (auth: Y)
Chain Length:125
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS31, RPS27a
Chain IDs:K (auth: b)
Chain Length:156
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS28, RPS28
Chain IDs:L (auth: c)
Chain Length:69
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS14, RPS29
Chain IDs:M (auth: d)
Chain Length:56
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:RACK1
Chain IDs:P (auth: g)
Chain Length:317
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polyribonucleotide
Molecule:18S ribosomal RNA
Chain IDs:N (auth: i)
Chain Length:1869
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Primary Citation
SARS-CoV-2 nsp1 mediates broad inhibition of translation in mammals.
Cell Rep 44 115696 115696 (2025)
PMID: 40359110 DOI: 10.1016/j.celrep.2025.115696

Abstact

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.

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