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- EMDB-72910: Class 2 SARS-CoV-2 Nsp1 Endonuclease Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-72910
TitleClass 2 SARS-CoV-2 Nsp1 Endonuclease Complex
Map datareconstruction of class 1 of active endonuclease complex comprised of purified 40S ribosomal subunits, CrPV IRES mRNA, and SARS-CoV-2 Nsp1-eIF3g Fusion protein.
Sample
  • Complex: Active SARS-CoV-2 Nsp1 endonuclease complex
    • Complex: SARS-CoV-2 Nsp1 endonuclease fused to human eIF3g RRM
    • Complex: human 40S ribosomal subunits
KeywordsSARS-CoV-2 Nsp1 eIF3g fusion / 40S ribosomal subunit / CrPV IRES / endonuclease complex / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsMichael MV / Shravani SB / Swapnil SD / Yong YX
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J Mol Biol / Year: 2026
Title: Nsp1 From Divergent Coronaviruses has Conserved Endonuclease Activity.
Authors: Michael Vetick / Shravani Balaji / Shannon Henry / Swapnil C Devarkar / Yong Xiong /
Abstract: All alpha- and beta-coronaviruses encode nonstructural protein 1 (Nsp1), a major virulence factor that restricts host gene expression. Herein, using Nsp1 from divergent alpha- and beta-coronaviruses ...All alpha- and beta-coronaviruses encode nonstructural protein 1 (Nsp1), a major virulence factor that restricts host gene expression. Herein, using Nsp1 from divergent alpha- and beta-coronaviruses (SARS-CoV-2, MERS-CoV, and HCoV-229E), we reveal all tested coronavirus Nsp1 proteins have intrinsic endonuclease activity. Furthermore, this endonuclease function is abolished when a conserved arginine-lysine motif in the N-terminal domain (NTD) is disrupted. For SARS-CoV-2 Nsp1, the eukaryotic Initiation Factor 3g (eIF3g) and the 40S ribosome act as cofactors for enhancing the endonuclease function, but these host factors are not conserved for the endonuclease function of MERS-CoV and HCoV-229E Nsp1. We propose that SARS-CoV-2 Nsp1 uses eIF3g and the 40S ribosome to enhance its affinity for RNA and target host mRNAs. Similar enhancement in endonuclease activity is observed when Nsp1 from SARS-CoV-2, MERS-CoV, and HCoV-229E are cis-tethered to an RNA-binding module. Collectively, our results show that endonuclease activity is intrinsic to Nsp1 across divergent coronavirus genera, and this endonuclease activity is likely targeted towards host mRNAs via a diverse set of host mRNA binding cofactors.
History
DepositionSep 27, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72910.png

Downloads & links

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Map

FileDownload / File: emd_72910.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationreconstruction of class 1 of active endonuclease complex comprised of purified 40S ribosomal subunits, CrPV IRES mRNA, and SARS-CoV-2 Nsp1-eIF3g Fusion protein.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 360 pix.
= 312.48 Å		0.87 Å/pix.
x 360 pix.
= 312.48 Å		0.87 Å/pix.
x 360 pix.
= 312.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.868 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0025
Minimum - Maximum-0.009683862 - 0.017264616
Average (Standard dev.)0.00010624571 (±0.00087615935)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 312.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A of reconstruction of class 1...

Fileemd_72910_half_map_1.map
AnnotationHalf map A of reconstruction of class 1 of active endonuclease complex comprised of purified 40S ribosomal subunits, CrPV IRES mRNA, and SARS-CoV-2 Nsp1-eIF3g Fusion protein.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of reconstruction of class 1...

Fileemd_72910_half_map_2.map
AnnotationHalf map B of reconstruction of class 1 of active endonuclease complex comprised of purified 40S ribosomal subunits, CrPV IRES mRNA, and SARS-CoV-2 Nsp1-eIF3g Fusion protein.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Active SARS-CoV-2 Nsp1 endonuclease complex

EntireName: Active SARS-CoV-2 Nsp1 endonuclease complex
Components
  • Complex: Active SARS-CoV-2 Nsp1 endonuclease complex
    • Complex: SARS-CoV-2 Nsp1 endonuclease fused to human eIF3g RRM
    • Complex: human 40S ribosomal subunits

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Supramolecule #1: Active SARS-CoV-2 Nsp1 endonuclease complex

SupramoleculeName: Active SARS-CoV-2 Nsp1 endonuclease complex / type: complex / ID: 1 / Parent: 0
Details: Comprised from coincubation of purified human 40S ribosomal subunits, CrPV IRES mRNA, and SARS-CoV-2 Nsp1 fused to human eIF3g RRM by 10aa GS linker.

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Supramolecule #2: SARS-CoV-2 Nsp1 endonuclease fused to human eIF3g RRM

SupramoleculeName: SARS-CoV-2 Nsp1 endonuclease fused to human eIF3g RRM / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: human 40S ribosomal subunits

SupramoleculeName: human 40S ribosomal subunits / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Details: 20mM HEPES(KOH)- pH7.5, 100mM KAc 2.5mM MgCl2, 1.0mM DTT, 0.25mM Spermidine 3HCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.24 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Software - details: 3D Flex Reconstruction / Number images used: 53000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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