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- EMDB-35751: Cryo-EM structure of SARS-CoV-2 spike protein in complex with dou... -

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Entry
Database: EMDB / ID: EMD-35751
TitleCryo-EM structure of SARS-CoV-2 spike protein in complex with double nAbs S2E12 and 3E2 (local refinement)
Map data
Sample
  • Complex: Cryo-EM structure of SARS-CoV-2 spike protein in complex with double nAbs 3E2 and 1C4
    • Complex: SARS-CoV-2 spike protein
    • Complex: nAb S2E12
    • Complex: nAb 3E2
KeywordsSARS-CoV-2 / Neutralizing antibody / Cryo-EM / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.79 Å
AuthorsSun H / Jiang Y / Zheng Q / Li S / Xia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Cell / Year: 2024
Title: Two antibodies show broad, synergistic neutralization against SARS-CoV-2 variants by inducing conformational change within the RBD.
Authors: Hui Sun / Tingting Deng / Yali Zhang / Yanling Lin / Yanan Jiang / Yichao Jiang / Yang Huang / Shuo Song / Lingyan Cui / Tingting Li / Hualong Xiong / Miaolin Lan / Liqin Liu / Yu Li / ...Authors: Hui Sun / Tingting Deng / Yali Zhang / Yanling Lin / Yanan Jiang / Yichao Jiang / Yang Huang / Shuo Song / Lingyan Cui / Tingting Li / Hualong Xiong / Miaolin Lan / Liqin Liu / Yu Li / Qianjiao Fang / Kunyu Yu / Wenling Jiang / Lizhi Zhou / Yuqiong Que / Tianying Zhang / Quan Yuan / Tong Cheng / Zheng Zhang / Hai Yu / Jun Zhang / Wenxin Luo / Shaowei Li / Qingbing Zheng / Ying Gu / Ningshao Xia /
Abstract: Continual evolution of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) virus has allowed for its gradual evasion of neutralizing antibodies (nAbs) produced in response to natural ...Continual evolution of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) virus has allowed for its gradual evasion of neutralizing antibodies (nAbs) produced in response to natural infection or vaccination. The rapid nature of these changes has incited a need for the development of superior broad nAbs (bnAbs) and/or the rational design of an antibody cocktail that can protect against the mutated virus strain. Here, we report two angiotensin-converting enzyme 2 competing nAbs-8H12 and 3E2-with synergistic neutralization but evaded by some Omicron subvariants. Cryo-electron microscopy reveals the two nAbs synergistic neutralizing virus through a rigorous pairing permitted by rearrangement of the 472-489 loop in the receptor-binding domain to avoid steric clashing. Bispecific antibodies based on these two nAbs tremendously extend the neutralizing breadth and restore neutralization against recent variants including currently dominant XBB.1.5. Together, these findings expand our understanding of the potential strategies for the neutralization of SARS-CoV-2 variants toward the design of broad-acting antibody therapeutics and vaccines.
History
DepositionMar 26, 2023-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35751.png

Downloads & links

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Map

FileDownload / File: emd_35751.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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.778 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.559092 - 0.8764873
Average (Standard dev.)-0.00018849432 (±0.008413243)
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_35751_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35751_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of SARS-CoV-2 spike protein in complex with dou...

EntireName: Cryo-EM structure of SARS-CoV-2 spike protein in complex with double nAbs 3E2 and 1C4
Components
  • Complex: Cryo-EM structure of SARS-CoV-2 spike protein in complex with double nAbs 3E2 and 1C4
    • Complex: SARS-CoV-2 spike protein
    • Complex: nAb S2E12
    • Complex: nAb 3E2

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Supramolecule #1: Cryo-EM structure of SARS-CoV-2 spike protein in complex with dou...

SupramoleculeName: Cryo-EM structure of SARS-CoV-2 spike protein in complex with double nAbs 3E2 and 1C4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

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Supramolecule #2: SARS-CoV-2 spike protein

SupramoleculeName: SARS-CoV-2 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 S2E12

SupramoleculeName: nAb S2E12 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: nAb 3E2

SupramoleculeName: nAb 3E2 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Mus musculus (house mouse)

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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: 1.1 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: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 195083
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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