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- EMDB-11323: SARS-CoV-2-Nsp1 bound to 43S Pre-initiation complex -

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Basic information

Entry
Database: EMDB / ID: EMD-11323
TitleSARS-CoV-2-Nsp1 bound to 43S Pre-initiation complex
Map data
Sample
  • Complex: SARS-CoV-2-Nsp1 bound to 43S Pre-initiation complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsSchubert K / Karousis ED / Jomaa A / Scaiola A / Echeverria B / Gurzeler L-A / Leibundgut M / Thiel V / Muehlemann O / Ban N
Funding support Switzerland, 3 items
OrganizationGrant numberCountry
Swiss National Science Foundation173085 Switzerland
Swiss National Science Foundation182831 Switzerland
Swiss National Science Foundation182341 Switzerland
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation.
Authors: Katharina Schubert / Evangelos D Karousis / Ahmad Jomaa / Alain Scaiola / Blanca Echeverria / Lukas-Adrian Gurzeler / Marc Leibundgut / Volker Thiel / Oliver Mühlemann / Nenad Ban /
Abstract: The SARS-CoV-2 non-structural protein 1 (Nsp1), also referred to as the host shutoff factor, suppresses host innate immune functions. By combining cryo-electron microscopy and biochemistry, we show ...The SARS-CoV-2 non-structural protein 1 (Nsp1), also referred to as the host shutoff factor, suppresses host innate immune functions. By combining cryo-electron microscopy and biochemistry, we show that SARS-CoV-2 Nsp1 binds to the human 40S subunit in ribosomal complexes, including the 43S pre-initiation complex and the non-translating 80S ribosome. The protein inserts its C-terminal domain into the mRNA channel, where it interferes with mRNA binding. We observe translation inhibition in the presence of Nsp1 in an in vitro translation system and in human cells. Based on the high-resolution structure of the 40S-Nsp1 complex, we identify residues of Nsp1 crucial for mediating translation inhibition. We further show that the full-length 5' untranslated region of the genomic viral mRNA stimulates translation in vitro, suggesting that SARS-CoV-2 combines global inhibition of translation by Nsp1 with efficient translation of the viral mRNA to allow expression of viral genes.
History
DepositionJul 7, 2020-
Header (metadata) releaseJul 22, 2020-
Map releaseJul 22, 2020-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11323.png

Downloads & links

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Map

FileDownload / File: emd_11323.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.512 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.015
Minimum - Maximum-0.07472511 - 0.14901075
Average (Standard dev.)0.00019690307 (±0.0025668254)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 604.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.5121.5121.512
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z604.800604.800604.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0750.1490.000

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Supplemental data

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Mask #1

Fileemd_11323_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

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Additional map: Map aligned to coordinates of SARS-CoV-2-Nsp1-40S complex (PDB:6ZOJ)

Fileemd_11323_additional.map
AnnotationMap aligned to coordinates of SARS-CoV-2-Nsp1-40S complex (PDB:6ZOJ)
Projections & Slices
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Additional map: Map aligned to coordinates of SARS-CoV-2-Nsp1-40S complex (PDB:6ZOJ)

Fileemd_11323_additional_1.map
AnnotationMap aligned to coordinates of SARS-CoV-2-Nsp1-40S complex (PDB:6ZOJ)
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_11323_half_map_1.map
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Half map: #2

Fileemd_11323_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : SARS-CoV-2-Nsp1 bound to 43S Pre-initiation complex

EntireName: SARS-CoV-2-Nsp1 bound to 43S Pre-initiation complex
Components
  • Complex: SARS-CoV-2-Nsp1 bound to 43S Pre-initiation complex

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Supramolecule #1: SARS-CoV-2-Nsp1 bound to 43S Pre-initiation complex

SupramoleculeName: SARS-CoV-2-Nsp1 bound to 43S Pre-initiation complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#36
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: 7.6
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5oa3

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18692

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