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- EMDB-74077: Cryo-EM Structure of Ab568 Fab in complex with SARS-CoV-2 6P Spike -

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Basic information

Entry
Database: EMDB / ID: EMD-74077
TitleCryo-EM Structure of Ab568 Fab in complex with SARS-CoV-2 6P Spike
Map dataCryo-EM Structure of Ab568 Fab in complex with SARS-CoV-2 6P Spike
Sample
  • Complex: Cryo-EM Structure of Ab568 Fab in complex with SARS-CoV-2 6P Spike
    • Complex: SARS-CoV-2 6P Spike
    • Complex: Ab568 Fab
KeywordsSARS-CoV-2 Spike / Antibody / Complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsGavor E / Bjorkman PJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01-AI165075 United States
Bill & Melinda Gates Foundation United States
CitationJournal: To Be Published
Title: Cryo-EM Structure of Ab568 Fab in complex with SARS-CoV-2 6P Spike
Authors: Skelly AN / Fan C / Keeffe JR / Okten A / Gavor E / Kreider EF / Ding W / Osbaldeston RA / Radford KM / Park Y / Cruickshank K / Liu W / Albertus A / McWilliams B / Russell RM / Konrath KM / ...Authors: Skelly AN / Fan C / Keeffe JR / Okten A / Gavor E / Kreider EF / Ding W / Osbaldeston RA / Radford KM / Park Y / Cruickshank K / Liu W / Albertus A / McWilliams B / Russell RM / Konrath KM / Yuan M / Gao H / Montefiori D / Ward A / Saag MS / Goepfert PA / Kulp DW / Shaw GM / Andrabi R / Weissman D / Wilen CB / Bjorkman PJ / Hahn BH
History
DepositionNov 26, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74077.png

Downloads & links

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Map

FileDownload / File: emd_74077.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM Structure of Ab568 Fab in complex with SARS-CoV-2 6P Spike
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 400 pix.
= 348. Å		0.87 Å/pix.
x 400 pix.
= 348. Å		0.87 Å/pix.
x 400 pix.
= 348. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0598
Minimum - Maximum-0.085799254 - 0.2880002
Average (Standard dev.)0.000004535749 (±0.012711365)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 348.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A of Cryo-EM Structure of Ab568...

Fileemd_74077_half_map_1.map
AnnotationHalf Map A of Cryo-EM Structure of Ab568 Fab in complex with SARS-CoV-2 6P Spike
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B of Cryo-EM Structure of Ab568...

Fileemd_74077_half_map_2.map
AnnotationHalf Map B of Cryo-EM Structure of Ab568 Fab in complex with SARS-CoV-2 6P Spike
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM Structure of Ab568 Fab in complex with SARS-CoV-2 6P Spike

EntireName: Cryo-EM Structure of Ab568 Fab in complex with SARS-CoV-2 6P Spike
Components
  • Complex: Cryo-EM Structure of Ab568 Fab in complex with SARS-CoV-2 6P Spike
    • Complex: SARS-CoV-2 6P Spike
    • Complex: Ab568 Fab

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Supramolecule #1: Cryo-EM Structure of Ab568 Fab in complex with SARS-CoV-2 6P Spike

SupramoleculeName: Cryo-EM Structure of Ab568 Fab in complex with SARS-CoV-2 6P Spike
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: SARS-CoV-2 6P Spike

SupramoleculeName: SARS-CoV-2 6P Spike / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: Ab568 Fab

SupramoleculeName: Ab568 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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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

Concentration3 mg/mL
BufferpH: 7.5 / Details: 150mM NaCl, 20mM Tris-HCL
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Particle selectionNumber selected: 410353
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4) / Number images used: 13421
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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