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- EMDB-15580: BA.1 SARS-CoV-2 Spike bound to mouse ACE2 (two up, full) -

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Basic information

Entry
Database: EMDB / ID: EMD-15580
TitleBA.1 SARS-CoV-2 Spike bound to mouse ACE2 (two up, full)
Map dataBA12
Sample
  • Complex: BA.1 SARS-CoV-2 Spike bound to mouse ACE2
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsLau K / Ni D / Beckert B / Nazarov S / Myasnikov A / Pojer F / Stahlberg H / Uchikawa E
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationNCCR transcure Switzerland
Citation
Journal: Plos Pathog. / Year: 2023
Title: Cryo-EM structures and binding of mouse and human ACE2 to SARS-CoV-2 variants of concern indicate that mutations enabling immune escape could expand host range
Authors: Ni D / Turelli P / Beckert B / Nazarov S / Uchikawa E / Myasnikov A / Pojer F / Trono D / Stahlberg H / Lau K
#1: Journal: Biorxiv / Year: 2023
Title: Cryo-EM structures and binding of mouse and human ACE2 to SARS-CoV-2 variants of concern indicate that mutations enabling immune escape could expand host range
Authors: Ni D / Turelli P / Beckert B / Nazarov S / Uchikawa E / Myasnikov A / Pojer F / Trono D / Stahlberg H / Lau K
History
DepositionAug 11, 2022-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateMar 15, 2023-
Current statusMar 15, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15580.png

Downloads & links

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Map

FileDownload / File: emd_15580.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBA12
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 350 pix.
= 362.985 Å		1.04 Å/pix.
x 350 pix.
= 362.985 Å		1.04 Å/pix.
x 350 pix.
= 362.985 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0371 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.33984149 - 0.81250864
Average (Standard dev.)2.5352751e-06 (±0.021379584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 362.985 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: BA12

Fileemd_15580_half_map_1.map
AnnotationBA12
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: BA12

Fileemd_15580_half_map_2.map
AnnotationBA12
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BA.1 SARS-CoV-2 Spike bound to mouse ACE2

EntireName: BA.1 SARS-CoV-2 Spike bound to mouse ACE2
Components
  • Complex: BA.1 SARS-CoV-2 Spike bound to mouse ACE2

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Supramolecule #1: BA.1 SARS-CoV-2 Spike bound to mouse ACE2

SupramoleculeName: BA.1 SARS-CoV-2 Spike bound to mouse ACE2 / type: complex / ID: 1 / Chimera: Yes / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 430 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 90 %
DetailsBA.1 SARS-CoV-2 Spike bound to mouse ACE2

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87727
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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