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- EMDB-15587: BA.4/5 SARS-CoV-2 Spike bound to human ACE2 (three up, full) -

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Basic information

Entry
Database: EMDB / ID: EMD-15587
TitleBA.4/5 SARS-CoV-2 Spike bound to human ACE2 (three up, full)
Map data45h
Sample
  • Complex: BA.4/5 SARS-CoV-2 Spike bound to human ACE2
    • Complex: BA.4/5 SARS-CoV-2 Spike
    • Complex: Human ACE2
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 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 13, 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_15587.png

Downloads & links

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Map

FileDownload / File: emd_15587.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation45h
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 360 pix.
= 365.184 Å		1.01 Å/pix.
x 360 pix.
= 365.184 Å		1.01 Å/pix.
x 360 pix.
= 365.184 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0144 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.37436858 - 0.7699231
Average (Standard dev.)-0.0004691559 (±0.019838342)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 365.184 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 45h

Fileemd_15587_additional_1.map
Annotation45h
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 45h

Fileemd_15587_half_map_1.map
Annotation45h
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 45h

Fileemd_15587_half_map_2.map
Annotation45h
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.4/5 SARS-CoV-2 Spike bound to human ACE2

EntireName: BA.4/5 SARS-CoV-2 Spike bound to human ACE2
Components
  • Complex: BA.4/5 SARS-CoV-2 Spike bound to human ACE2
    • Complex: BA.4/5 SARS-CoV-2 Spike
    • Complex: Human ACE2

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Supramolecule #1: BA.4/5 SARS-CoV-2 Spike bound to human ACE2

SupramoleculeName: BA.4/5 SARS-CoV-2 Spike bound to human ACE2 / type: complex / ID: 1 / Chimera: Yes / Parent: 0
Molecular weightTheoretical: 430 KDa

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Supramolecule #2: BA.4/5 SARS-CoV-2 Spike

SupramoleculeName: BA.4/5 SARS-CoV-2 Spike / type: complex / ID: 2 / Chimera: Yes / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: Human ACE2

SupramoleculeName: Human ACE2 / type: complex / ID: 3 / Chimera: Yes / 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
VitrificationCryogen name: ETHANE
DetailsBA.4/5 SARS-CoV-2 Spike bound to human ACE2

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 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: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94718
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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