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- EMDB-36949: Neutralization antibody ZCP4D5 bound with SARS-CoV-2 Omicron BA.5... -

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Basic information

Entry
Database: EMDB / ID: EMD-36949
TitleNeutralization antibody ZCP4D5 bound with SARS-CoV-2 Omicron BA.5 spike trimer
Map data
Sample
  • Complex: Neutralization antibody ZCP4D5 bound with SARS-CoV-2 Omicron BA.5 Spike trimer
KeywordsSARS-CoV-2 / neutralization antibody / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsTang B / Dang S
Funding support Hong Kong, 1 items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: To Be Published
Title: Neutralization antibody ZCP4D5 bound with SARS-CoV-2 Omicron BA.5 spike trimer
Authors: Tang B / Dang S
History
DepositionJul 30, 2023-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36949.png

Downloads & links

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Map

FileDownload / File: emd_36949.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å

Surface

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.093793295 - 0.4028696
Average (Standard dev.)0.0016883498 (±0.018496754)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_36949_additional_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_36949_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36949_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Neutralization antibody ZCP4D5 bound with SARS-CoV-2 Omicron BA.5...

EntireName: Neutralization antibody ZCP4D5 bound with SARS-CoV-2 Omicron BA.5 Spike trimer
Components
  • Complex: Neutralization antibody ZCP4D5 bound with SARS-CoV-2 Omicron BA.5 Spike trimer

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Supramolecule #1: Neutralization antibody ZCP4D5 bound with SARS-CoV-2 Omicron BA.5...

SupramoleculeName: Neutralization antibody ZCP4D5 bound with SARS-CoV-2 Omicron BA.5 Spike trimer
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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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 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: 2.5 µm / Nominal defocus min: 1.0 µm
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: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77000
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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