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- EMDB-34604: Immune complex of W328-6H2 Fab binding the RBD of SARS-CoV-1 2P s... -

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Entry
Database: EMDB / ID: EMD-34604
TitleImmune complex of W328-6H2 Fab binding the RBD of SARS-CoV-1 2P spike protein
Map dataImmune complex of W328-6H2 Fab binding the RBD of SARS-CoV-1 2P spike protein
Sample
  • Complex: SARS-CoV-1 2P in complex with W328-6H2 Fab
    • Complex: Severe acute respiratory syndrome coronavirus 1-2P
    • Complex: W328-6H2 Fab
KeywordsComplex / SARS-CoV-1 / antibody / Homo sapiens / RBD / VIRAL PROTEIN
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsZhu JY / Zhou BN
Funding support China, 2 items
OrganizationGrant numberCountry
Other governmentE1l0511ZX China
Other governmentE1XT2611FT China
CitationJournal: Immunity / Year: 2023
Title: Dissecting the intricacies of human antibody responses to SARS-CoV-1 and SARS-CoV-2 infection.
Authors: Ruoke Wang / Yang Han / Rui Zhang / Jiayi Zhu / Xuanyu Nan / Yaping Liu / Ziqing Yang / Bini Zhou / Jinfang Yu / Zichun Lin / Jinqian Li / Peng Chen / Yangjunqi Wang / Yujie Li / Dongsheng ...Authors: Ruoke Wang / Yang Han / Rui Zhang / Jiayi Zhu / Xuanyu Nan / Yaping Liu / Ziqing Yang / Bini Zhou / Jinfang Yu / Zichun Lin / Jinqian Li / Peng Chen / Yangjunqi Wang / Yujie Li / Dongsheng Liu / Xuanling Shi / Xinquan Wang / Qi Zhang / Yuhe R Yang / Taisheng Li / Linqi Zhang /
Abstract: The 2003 severe acute respiratory syndrome coronavirus (SARS-CoV-1) causes more severe disease than SARS-CoV-2, which is responsible for COVID-19. However, our understanding of antibody response to ...The 2003 severe acute respiratory syndrome coronavirus (SARS-CoV-1) causes more severe disease than SARS-CoV-2, which is responsible for COVID-19. However, our understanding of antibody response to SARS-CoV-1 infection remains incomplete. Herein, we studied the antibody responses in 25 SARS-CoV-1 convalescent patients. Plasma neutralization was higher and lasted longer in SARS-CoV-1 patients than in severe SARS-CoV-2 patients. Among 77 monoclonal antibodies (mAbs) isolated, 60 targeted the receptor-binding domain (RBD) and formed 7 groups (RBD-1 to RBD-7) based on their distinct binding and structural profiles. Notably, RBD-7 antibodies bound to a unique RBD region interfaced with the N-terminal domain of the neighboring protomer (NTD proximal) and were more prevalent in SARS-CoV-1 patients. Broadly neutralizing antibodies for SARS-CoV-1, SARS-CoV-2, and bat and pangolin coronaviruses were also identified. These results provide further insights into the antibody response to SARS-CoV-1 and inform the design of more effective strategies against diverse human and animal coronaviruses.
History
DepositionOct 26, 2022-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34604.png

Downloads & links

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Map

FileDownload / File: emd_34604.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationImmune complex of W328-6H2 Fab binding the RBD of SARS-CoV-1 2P spike protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.21 Å/pix.
x 192 pix.
= 424.32 Å		2.21 Å/pix.
x 192 pix.
= 424.32 Å		2.21 Å/pix.
x 192 pix.
= 424.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0202
Minimum - Maximum-0.028504193 - 0.058226645
Average (Standard dev.)0.0002484983 (±0.0043682037)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 424.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Immune complex of W328-6H2 Fab binding the RBD...

Fileemd_34604_half_map_1.map
AnnotationImmune complex of W328-6H2 Fab binding the RBD of SARS-CoV-1 2P spike protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Immune complex of W328-6H2 Fab binding the RBD...

Fileemd_34604_half_map_2.map
AnnotationImmune complex of W328-6H2 Fab binding the RBD of SARS-CoV-1 2P spike protein
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-1 2P in complex with W328-6H2 Fab

EntireName: SARS-CoV-1 2P in complex with W328-6H2 Fab
Components
  • Complex: SARS-CoV-1 2P in complex with W328-6H2 Fab
    • Complex: Severe acute respiratory syndrome coronavirus 1-2P
    • Complex: W328-6H2 Fab

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Supramolecule #1: SARS-CoV-1 2P in complex with W328-6H2 Fab

SupramoleculeName: SARS-CoV-1 2P in complex with W328-6H2 Fab / type: complex / ID: 1 / Parent: 0
Details: Immune complex of W328-6H2 Fab binding the RBD of SARS-CoV-1 2P spike protein
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Severe acute respiratory syndrome coronavirus 1-2P

SupramoleculeName: Severe acute respiratory syndrome coronavirus 1-2P / type: complex / ID: 2 / Parent: 1 / Details: SARS-CoV-1 2P
Source (natural)Organism: Severe acute respiratory syndrome coronavirus

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Supramolecule #3: W328-6H2 Fab

SupramoleculeName: W328-6H2 Fab / type: complex / ID: 3 / Parent: 1 / Details: W328-6H2 Fab
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.015 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Acetate

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Electron microscopy

MicroscopeJEOL 2100F
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: OTHER / Average electron dose: 25.0 e/Å2

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5x58

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 301

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