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- EMDB-45548: Cryo-EM Refinement of Antibody 19-77 in complex with SARS-CoV-2 p... -

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Basic information

Entry
Database: EMDB / ID: EMD-45548
TitleCryo-EM Refinement of Antibody 19-77 in complex with SARS-CoV-2 prefusion spike
Map dataRefinement of Antibody 19-77 in complex with SARS-CoV-2 prefusion spike
Sample
  • Complex: Antibody 19-77 in complex with prefusion SARS-CoV-2 Spike glycoprotein
KeywordsNeutralizing Antibody / Viral Fusion Protein / SARS-CoV-2 / VIRAL PROTEIN-IMMUNE SYSTEM complex / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsCasner RG / Shapiro L
Funding support China, 1 items
OrganizationGrant numberCountry
Jack Ma Foundation China
CitationJournal: To Be Published
Title: More SARS-CoV-2 antibodies
Authors: Casner RG
History
DepositionJun 27, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45548.png

Downloads & links

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Map

FileDownload / File: emd_45548.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefinement of Antibody 19-77 in complex with SARS-CoV-2 prefusion spike
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 440 pix.
= 365.2 Å		0.83 Å/pix.
x 440 pix.
= 365.2 Å		0.83 Å/pix.
x 440 pix.
= 365.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.957906 - 2.125655
Average (Standard dev.)-0.00052520493 (±0.045175914)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 365.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half a

Fileemd_45548_half_map_1.map
Annotationhalf a
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half b

Fileemd_45548_half_map_2.map
Annotationhalf b
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Antibody 19-77 in complex with prefusion SARS-CoV-2 Spike glycoprotein

EntireName: Antibody 19-77 in complex with prefusion SARS-CoV-2 Spike glycoprotein
Components
  • Complex: Antibody 19-77 in complex with prefusion SARS-CoV-2 Spike glycoprotein

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Supramolecule #1: Antibody 19-77 in complex with prefusion SARS-CoV-2 Spike glycoprotein

SupramoleculeName: Antibody 19-77 in complex with prefusion SARS-CoV-2 Spike glycoprotein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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

Concentration1 mg/mL
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: 58.0 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 329845
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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