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- EMDB-34264: Cryo-EM map of Omicron BA.5 S protein in complex with S2L20 focus... -

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Basic information

Entry
Database: EMDB / ID: EMD-34264
TitleCryo-EM map of Omicron BA.5 S protein in complex with S2L20 focused on NTD_S2L20 sub-complex
Map data
Sample
  • Complex: Cryo-EM map of Omicron BA.5 S protein in complex with S2L20 focused on NTD_S2L20 sub-complex
    • Complex: S protein of Omicron BA.5 variant
    • Complex: S2L20
KeywordsSARS-CoV-2 / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsXia LY / Zhang YY / Zhou Q
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32022037 China
National Natural Science Foundation of China (NSFC)81803429 China
CitationJournal: Cell Discov / Year: 2023
Title: Comprehensive structural analysis reveals broad-spectrum neutralizing antibodies against SARS-CoV-2 Omicron variants.
Authors: Xiangyang Chi / Lingyun Xia / Guanying Zhang / Ximin Chi / Bangdong Huang / Yuanyuan Zhang / Zhengshan Chen / Jin Han / Liushu Wu / Zeya Li / Hancong Sun / Ping Huang / Changming Yu / Wei Chen / Qiang Zhou /
Abstract: The pandemic of COVID-19 caused by SARS-CoV-2 continues to spread around the world. Mutant strains of SARS-CoV-2 are constantly emerging. At present, Omicron variants have become mainstream. In this ...The pandemic of COVID-19 caused by SARS-CoV-2 continues to spread around the world. Mutant strains of SARS-CoV-2 are constantly emerging. At present, Omicron variants have become mainstream. In this work, we carried out a systematic and comprehensive analysis of the reported spike protein antibodies, counting the epitopes and genotypes of these antibodies. We further comprehensively analyzed the impact of Omicron mutations on antibody epitopes and classified these antibodies according to their binding patterns. We found that the epitopes of the H-RBD class antibodies were significantly less affected by Omicron mutations than other classes. Binding and virus neutralization experiments showed that such antibodies could effectively inhibit the immune escape of Omicron. Cryo-EM results showed that this class of antibodies utilized a conserved mechanism to neutralize SARS-CoV-2. Our results greatly help us deeply understand the impact of Omicron mutations. Meanwhile, it also provides guidance and insights for developing Omicron antibodies and vaccines.
History
DepositionSep 8, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJul 12, 2023-
Current statusJul 12, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34264.png

Downloads & links

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Map

FileDownload / File: emd_34264.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 344.64 Å		1.08 Å/pix.
x 320 pix.
= 344.64 Å		1.08 Å/pix.
x 320 pix.
= 344.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.077 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.85
Minimum - Maximum-4.5837946 - 6.651195
Average (Standard dev.)0.0049624047 (±0.080992416)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 344.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34264_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_34264_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 : Cryo-EM map of Omicron BA.5 S protein in complex with S2L20 focus...

EntireName: Cryo-EM map of Omicron BA.5 S protein in complex with S2L20 focused on NTD_S2L20 sub-complex
Components
  • Complex: Cryo-EM map of Omicron BA.5 S protein in complex with S2L20 focused on NTD_S2L20 sub-complex
    • Complex: S protein of Omicron BA.5 variant
    • Complex: S2L20

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Supramolecule #1: Cryo-EM map of Omicron BA.5 S protein in complex with S2L20 focus...

SupramoleculeName: Cryo-EM map of Omicron BA.5 S protein in complex with S2L20 focused on NTD_S2L20 sub-complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: S protein of Omicron BA.5 variant

SupramoleculeName: S protein of Omicron BA.5 variant / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: S2L20

SupramoleculeName: S2L20 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 162448
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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