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- EMDB-44680: SARS-Cov-2 spike glycoprotein with 1 RBD up -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-44680
TitleSARS-Cov-2 spike glycoprotein with 1 RBD up
Map datasharpened map of SARS-2 S glycoprotein in open state
Sample
  • Complex: SARS-CoV-2 S glycoprotein containing 2P mutations with 1 RBD up
KeywordsSARS-CoV-2 / open state / coronavirus / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsTorrents de la Pena A / Sewall LM / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI136621C3 United States
Bill & Melinda Gates FoundationINV-002916 United States
CitationJournal: Nat Biomed Eng / Year: 2025
Title: Rapid and High-Throughput Imaging of Immune Complexes Using Microfluidics and Single Particle Electron Microscopy
Authors: Sewall LM / de Paiva Froes Rocha R / Gibson G / Louie M / Xie Z / Bangaru S / Tran AS / Ozorowski G / Mohanty S / Beutler N / Burton DR / Shaw AC / Batista FD / Chocarro Ruiz B / Torrents de la Pena A / Ward AB
History
DepositionMay 2, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44680.png

Downloads & links

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Map

FileDownload / File: emd_44680.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map of SARS-2 S glycoprotein in open state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 400 pix.
= 460. Å		1.15 Å/pix.
x 400 pix.
= 460. Å		1.15 Å/pix.
x 400 pix.
= 460. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.0703937 - 1.9590513
Average (Standard dev.)-0.00039592056 (±0.04684334)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 460.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44680_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map of SARS-2 S glycoprotein in open state

Fileemd_44680_additional_1.map
Annotationunsharpened map of SARS-2 S glycoprotein in open state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map SARS-2 S glycoprotein in open state

Fileemd_44680_half_map_1.map
Annotationhalf map SARS-2 S glycoprotein in open state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of SARS-2 S glycoprotein in open state

Fileemd_44680_half_map_2.map
Annotationhalf map of SARS-2 S glycoprotein in open state
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 S glycoprotein containing 2P mutations with 1 RBD up

EntireName: SARS-CoV-2 S glycoprotein containing 2P mutations with 1 RBD up
Components
  • Complex: SARS-CoV-2 S glycoprotein containing 2P mutations with 1 RBD up

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Supramolecule #1: SARS-CoV-2 S glycoprotein containing 2P mutations with 1 RBD up

SupramoleculeName: SARS-CoV-2 S glycoprotein containing 2P mutations with 1 RBD up
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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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

Concentration0.02 mg/mL
BufferpH: 7.4
GridModel: EMS Lacey Carbon / Material: GRAPHENE OXIDE / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 2.5 seconds blot time, 30sec waiting time, blot force 1.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 9755
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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