9NPX image
Deposition Date 2025-03-11
Release Date 2025-06-11
Last Version Date 2025-06-11
Entry Detail
PDB ID:
9NPX
Keywords:
Title:
SARS-CoV-2 nsp1 bound to the Rhinolophus lepidus 40S ribosomal subunit (local refinement of the 40S body)
Biological Source:
Host 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 S2
Chain IDs:A
Chain Length:84
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS3, RPS3
Chain IDs:X (auth: B)
Chain Length:243
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3a
Chain IDs:V (auth: C)
Chain Length:264
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4, X isoform
Chain IDs:B (auth: D)
Chain Length:263
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Chain IDs:C (auth: F)
Chain Length:249
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Chain IDs:S (auth: G)
Chain Length:194
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Chain IDs:D (auth: H)
Chain Length:208
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9
Chain IDs:E (auth: I)
Chain Length:1869
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11
Chain IDs:T (auth: K)
Chain Length:113
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Chain IDs:F (auth: M)
Chain Length:151
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14
Chain IDs:G (auth: N)
Chain Length:151
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15a
Chain IDs:H (auth: P)
Chain Length:130
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17
Chain IDs:I (auth: R)
Chain Length:135
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21
Chain IDs:J (auth: V)
Chain Length:84
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23
Chain IDs:K (auth: W)
Chain Length:143
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Chain IDs:L (auth: X)
Chain Length:130
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26
Chain IDs:M (auth: Z)
Chain Length:115
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Chain IDs:N (auth: a)
Chain Length:84
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Chain IDs:U (auth: e)
Chain Length:61
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41
Chain IDs:O (auth: f)
Chain Length:249
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein SA
Chain IDs:P (auth: h)
Chain Length:208
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polyribonucleotide
Molecule:18S ribosomal RNA
Chain IDs:W (auth: i)
Chain Length:1869
Number of Molecules:1
Biological Source:Rhinolophus lepidus
Polymer Type:polypeptide(L)
Molecule:Host translation inhibitor nsp1
Gene (Uniprot):rep
Chain IDs:Q (auth: j)
Chain Length:180
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 1
Gene (Uniprot):EIF1
Chain IDs:R (auth: k)
Chain Length:113
Number of Molecules:1
Biological Source:Homo sapiens
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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