[English] 日本語
Yorodumi
- PDB-9npy: SARS-CoV-2 nsp1 bound to the Rhinolophus lepidus 40S ribosome (lo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9npy
TitleSARS-CoV-2 nsp1 bound to the Rhinolophus lepidus 40S ribosome (local refinement of the 40S head)
Components
  • (40S ribosomal protein ...) x 14
  • 18S ribosomal RNA
  • RACK1
KeywordsRIBOSOME / SARS-CoV-2 / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesRhinolophus lepidus (bat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsGen, R. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell Rep / Year: 2025
Title: SARS-CoV-2 nsp1 mediates broad inhibition of translation in mammals.
Authors: Risako Gen / Amin Addetia / Daniel Asarnow / Young-Jun Park / Joel Quispe / Matthew C Chan / Jack T Brown / Jimin Lee / Melody G Campbell / Christopher P Lapointe / David Veesler /
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 ...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.
History
DepositionMar 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Data collection / Other / Category: em_admin / pdbx_SG_project / pdbx_database_status
Item: _em_admin.last_update / _pdbx_database_status.SG_entry
Revision 1.1Jul 30, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: 40S ribosomal protein uS3, RPS3
J: 40S ribosomal protein eS10, RPS10
L: 40S ribosomal protein eS12, RPS12
O: 40S ribosomal protein uS19, RPS15
Q: 40S ribosomal protein uS9, RPS16
R: 40S ribosomal protein eS17, RPS17
S: 40S ribosomal protein uS13, RPS18
T: 40S ribosomal protein eS19, RPS19
U: 40S ribosomal protein uS10, RPS20
Y: 40S ribosomal protein eS25, RPS25
b: 40S ribosomal protein eS31, RPS27a
c: 40S ribosomal protein eS28, RPS28
d: 40S ribosomal protein uS14, RPS29
i: 18S ribosomal RNA
E: 40S ribosomal protein uS7, RPS5
g: RACK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)865,51748
Polymers864,52316
Non-polymers99332
Water14,898827
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
40S ribosomal protein ... , 14 types, 14 molecules BJLOQRSTUYbcdE

#1: Protein 40S ribosomal protein uS3, RPS3


Mass: 26715.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhinolophus lepidus (bat)
#2: Protein 40S ribosomal protein eS10, RPS10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhinolophus lepidus (bat)
#3: Protein 40S ribosomal protein eS12, RPS12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhinolophus lepidus (bat)
#4: Protein 40S ribosomal protein uS19, RPS15


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhinolophus lepidus (bat)
#5: Protein 40S ribosomal protein uS9, RPS16


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhinolophus lepidus (bat)
#6: Protein 40S ribosomal protein eS17, RPS17


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhinolophus lepidus (bat)
#7: Protein 40S ribosomal protein uS13, RPS18


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhinolophus lepidus (bat)
#8: Protein 40S ribosomal protein eS19, RPS19


Mass: 16104.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhinolophus lepidus (bat)
#9: Protein 40S ribosomal protein uS10, RPS20


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhinolophus lepidus (bat)
#10: Protein 40S ribosomal protein eS25, RPS25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhinolophus lepidus (bat)
#11: Protein 40S ribosomal protein eS31, RPS27a


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhinolophus lepidus (bat)
#12: Protein 40S ribosomal protein eS28, RPS28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhinolophus lepidus (bat)
#13: Protein 40S ribosomal protein uS14, RPS29


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhinolophus lepidus (bat)
#15: Protein 40S ribosomal protein uS7, RPS5


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhinolophus lepidus (bat)

-
RNA chain / Protein , 2 types, 2 molecules ig

#14: RNA chain 18S ribosomal RNA


Mass: 603611.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhinolophus lepidus (bat)
#16: Protein RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhinolophus lepidus (bat)

-
Non-polymers , 4 types, 859 molecules

#17: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Mg
#18: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#19: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#20: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 827 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1SARS-CoV-2 nsp1-Rhinolophus lepidus ribosome complex, head mapRIBOSOME#1-#160MULTIPLE SOURCES
2Rhinolophus lepidus ribosomeORGANELLE OR CELLULAR COMPONENT#1-#161NATURAL
3SARS-CoV-2 nsp1COMPLEX1RECOMBINANT
4Eukaryotic translation initiation factor 1COMPLEX1RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Rhinolophus lepidus (bat)188570
33Severe acute respiratory syndrome coronavirus 22697049
44Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Escherichia coli (E. coli)562
24Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 30.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1205667 / Symmetry type: POINT
RefinementHighest resolution: 2.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00525762
ELECTRON MICROSCOPYf_angle_d0.52737215
ELECTRON MICROSCOPYf_dihedral_angle_d19.24212186
ELECTRON MICROSCOPYf_chiral_restr0.044634
ELECTRON MICROSCOPYf_plane_restr0.0042927

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more