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- EMDB-26560: Cryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike protein in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-26560
TitleCryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike protein in complex with bebtelovimab
Map dataCryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike protein in complex with bebtelovimab
Sample
  • Complex: SARS-CoV-2 Alpha (B.1.1.7) spike protein in complex with bebtelovimab
    • Complex: SARS-CoV-2 Alpha (B.1.1.7) spike protein
      • Complex: Monoclonal antibody bebtelovimab
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsPankaj P / Robb C / Scortecci JF
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)D18AC00002 United States
CitationJournal: To Be Published
Title: LY-CoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variants
Authors: Pankaj P
History
DepositionMar 30, 2022-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateApr 12, 2023-
Current statusApr 12, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26560.png

Downloads & links

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Map

FileDownload / File: emd_26560.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike protein in complex with bebtelovimab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 400 pix.
= 392. Å		0.98 Å/pix.
x 400 pix.
= 392. Å		0.98 Å/pix.
x 400 pix.
= 392. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0171
Minimum - Maximum-0.09561 - 0.15550937
Average (Standard dev.)7.4635704e-05 (±0.003571756)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 392.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike protein...

Fileemd_26560_half_map_1.map
AnnotationCryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike protein in complex with bebtelovimab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike protein...

Fileemd_26560_half_map_2.map
AnnotationCryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike protein in complex with bebtelovimab
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 Alpha (B.1.1.7) spike protein in complex with bebtelovimab

EntireName: SARS-CoV-2 Alpha (B.1.1.7) spike protein in complex with bebtelovimab
Components
  • Complex: SARS-CoV-2 Alpha (B.1.1.7) spike protein in complex with bebtelovimab
    • Complex: SARS-CoV-2 Alpha (B.1.1.7) spike protein
      • Complex: Monoclonal antibody bebtelovimab

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Supramolecule #1: SARS-CoV-2 Alpha (B.1.1.7) spike protein in complex with bebtelovimab

SupramoleculeName: SARS-CoV-2 Alpha (B.1.1.7) spike protein in complex with bebtelovimab
type: complex / ID: 1 / Chimera: Yes / Parent: 0

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Supramolecule #2: SARS-CoV-2 Alpha (B.1.1.7) spike protein

SupramoleculeName: SARS-CoV-2 Alpha (B.1.1.7) spike protein / type: complex / ID: 2 / Chimera: Yes / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: Monoclonal antibody bebtelovimab

SupramoleculeName: Monoclonal antibody bebtelovimab / type: complex / ID: 3 / Chimera: Yes / Parent: 2
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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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