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- EMDB-29374: Structure of SARS-CoV2 spike protein -

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Basic information

Entry
Database: EMDB / ID: EMD-29374
TitleStructure of SARS-CoV2 spike protein
Map data
Sample
  • Complex: SARS-CoV-2 spike with D994Q mutation
Biological speciesSevere acute respiratory syndrome coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsMou Z / Tan TJC / Lei R / Wu NC / Dai X
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI167910 United States
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)AT011966 United States
Michelson Prizes for Human Immunology and Vaccine Research United States
Searle Scholars Program United States
CitationJournal: Nat Commun / Year: 2023
Title: High-throughput identification of prefusion-stabilizing mutations in SARS-CoV-2 spike.
Authors: Timothy J C Tan / Zongjun Mou / Ruipeng Lei / Wenhao O Ouyang / Meng Yuan / Ge Song / Raiees Andrabi / Ian A Wilson / Collin Kieffer / Xinghong Dai / Kenneth A Matreyek / Nicholas C Wu /
Abstract: Designing prefusion-stabilized SARS-CoV-2 spike is critical for the effectiveness of COVID-19 vaccines. All COVID-19 vaccines in the US encode spike with K986P/V987P mutations to stabilize its ...Designing prefusion-stabilized SARS-CoV-2 spike is critical for the effectiveness of COVID-19 vaccines. All COVID-19 vaccines in the US encode spike with K986P/V987P mutations to stabilize its prefusion conformation. However, contemporary methods on engineering prefusion-stabilized spike immunogens involve tedious experimental work and heavily rely on structural information. Here, we establish a systematic and unbiased method of identifying mutations that concomitantly improve expression and stabilize the prefusion conformation of the SARS-CoV-2 spike. Our method integrates a fluorescence-based fusion assay, mammalian cell display technology, and deep mutational scanning. As a proof-of-concept, we apply this method to a region in the S2 domain that includes the first heptad repeat and central helix. Our results reveal that besides K986P and V987P, several mutations simultaneously improve expression and significantly lower the fusogenicity of the spike. As prefusion stabilization is a common challenge for viral immunogen design, this work will help accelerate vaccine development against different viruses.
History
DepositionJan 5, 2023-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateApr 26, 2023-
Current statusApr 26, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29374.png

Downloads & links

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Map

FileDownload / File: emd_29374.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 360 pix.
= 237.6 Å		0.66 Å/pix.
x 360 pix.
= 237.6 Å		0.66 Å/pix.
x 360 pix.
= 237.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.46453083 - 0.9363055
Average (Standard dev.)0.002356058 (±0.037677746)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 237.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_29374_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29374_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 spike with D994Q mutation

EntireName: SARS-CoV-2 spike with D994Q mutation
Components
  • Complex: SARS-CoV-2 spike with D994Q mutation

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Supramolecule #1: SARS-CoV-2 spike with D994Q mutation

SupramoleculeName: SARS-CoV-2 spike with D994Q mutation / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus
Molecular weightTheoretical: 540 KDa

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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

Concentration1 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 140183
Initial angle assignmentType: COMMON LINE

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