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- EMDB-35789: Cryo-EM structure of SARS-CoV-2 BA.4/5 spike protein in complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-35789
TitleCryo-EM structure of SARS-CoV-2 BA.4/5 spike protein in complex with 1G11 (state 2)
Map data
Sample
  • Complex: SARS-CoV-2 BA.4/5 spike protein in complex with 1G11
    • Complex: SARS-CoV-2 BA.4/5 spike protein
    • Complex: nAb 1G11
KeywordsSARS-CoV-2 / Neutralizing antibody / Cryo-EM / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsSun H / Jiang Y / Zheng Z / Zheng Q / Li S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Virol / Year: 2023
Title: Structural basis for broad neutralization of human antibody against Omicron sublineages and evasion by XBB variant.
Authors: Hui Sun / Yizhen Wang / Xiuting Chen / Yanan Jiang / Siling Wang / Yang Huang / Liqin Liu / Yu Li / Miaolin Lan / Huilin Guo / Quan Yuan / Yali Zhang / Tingting Li / Hai Yu / Ying Gu / Jun ...Authors: Hui Sun / Yizhen Wang / Xiuting Chen / Yanan Jiang / Siling Wang / Yang Huang / Liqin Liu / Yu Li / Miaolin Lan / Huilin Guo / Quan Yuan / Yali Zhang / Tingting Li / Hai Yu / Ying Gu / Jun Zhang / Shaowei Li / Zizheng Zheng / Qingbing Zheng / Ningshao Xia /
Abstract: The ongoing COVID-19 pandemic has been characterized by the emergence of new SARS-CoV-2 variants including the highly transmissible Omicron XBB sublineages, which have shown significant resistance to ...The ongoing COVID-19 pandemic has been characterized by the emergence of new SARS-CoV-2 variants including the highly transmissible Omicron XBB sublineages, which have shown significant resistance to neutralizing antibodies (nAbs). This resistance has led to decreased vaccine effectiveness and therefore result in breakthrough infections and reinfections, which continuously threaten public health. To date, almost all available therapeutic nAbs, including those authorized under Emergency Use Authorization nAbs that were previously clinically useful against early strains, have recently been found to be ineffective against newly emerging variants. In this study, we provide a comprehensive structural basis about how the Class 3 nAbs, including 1G11 in this study and noted LY-CoV1404, are evaded by the newly emerged SARS-CoV-2 variants.
History
DepositionMar 31, 2023-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35789.png

Downloads & links

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Map

FileDownload / File: emd_35789.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.78 Å/pix.
x 576 pix.
= 448.128 Å		0.78 Å/pix.
x 576 pix.
= 448.128 Å		0.78 Å/pix.
x 576 pix.
= 448.128 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.778 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.08854584 - 0.25025347
Average (Standard dev.)-0.00006161597 (±0.0066847987)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 448.128 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35789_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35789_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 BA.4/5 spike protein in complex with 1G11

EntireName: SARS-CoV-2 BA.4/5 spike protein in complex with 1G11
Components
  • Complex: SARS-CoV-2 BA.4/5 spike protein in complex with 1G11
    • Complex: SARS-CoV-2 BA.4/5 spike protein
    • Complex: nAb 1G11

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Supramolecule #1: SARS-CoV-2 BA.4/5 spike protein in complex with 1G11

SupramoleculeName: SARS-CoV-2 BA.4/5 spike protein in complex with 1G11 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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

SupramoleculeName: SARS-CoV-2 BA.4/5 spike protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: nAb 1G11

SupramoleculeName: nAb 1G11 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
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 TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k 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: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 144396
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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