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- EMDB-64594: The binding of a C-based single-domain antibody stabilizes spikes... -

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Basic information

Entry
Database: EMDB / ID: EMD-64594
TitleThe binding of a C-based single-domain antibody stabilizes spikes of SARS-CoV2 (BA.5) in all-RBD-up conformation
Map data
Sample
  • Complex: The complex formed by SARS-CoV2 BA.5 spike protein and a single-domain antibody
    • Complex: Spike glycoprotein of SARS-CoV2 BA.5
    • Complex: single-domain antibody
KeywordsSARS-CoV2 / RBD / Single-domain antibody / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.22 Å
AuthorsWu B / Rao G / Cao S / Gong R
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170949 China
CitationJournal: To Be Published
Title: A C-based single-domain antibody broadly neutralizes SARS-CoV-2 and its variants through novel recognition of conserved regions in RBD
Authors: Wu B / Rao G / Zhang H / Yi Y / Zhao S / Qin Y / Li M / Chen L / Zhang Z / Zhang Z / Mu J / Chiu S / Cao S / Gong R
History
DepositionMay 14, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64594.png

Downloads & links

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Map

FileDownload / File: emd_64594.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 600 pix.
= 570. Å		0.95 Å/pix.
x 600 pix.
= 570. Å		0.95 Å/pix.
x 600 pix.
= 570. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.1430934 - 0.43782842
Average (Standard dev.)0.00014339488 (±0.012668603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 570.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_64594_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_64594_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 : The complex formed by SARS-CoV2 BA.5 spike protein and a single-d...

EntireName: The complex formed by SARS-CoV2 BA.5 spike protein and a single-domain antibody
Components
  • Complex: The complex formed by SARS-CoV2 BA.5 spike protein and a single-domain antibody
    • Complex: Spike glycoprotein of SARS-CoV2 BA.5
    • Complex: single-domain antibody

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Supramolecule #1: The complex formed by SARS-CoV2 BA.5 spike protein and a single-d...

SupramoleculeName: The complex formed by SARS-CoV2 BA.5 spike protein and a single-domain antibody
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #2: Spike glycoprotein of SARS-CoV2 BA.5

SupramoleculeName: Spike glycoprotein of SARS-CoV2 BA.5 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: single-domain antibody

SupramoleculeName: single-domain antibody / type: complex / ID: 3 / Parent: 1
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

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k 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: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24261
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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