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- EMDB-25150: Antibody N3-1 bound to SARS-CoV-2 spike -

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Basic information

Entry
Database: EMDB / ID: EMD-25150
TitleAntibody N3-1 bound to SARS-CoV-2 spike
Map data
Sample
  • Complex: Complex of N3-1 bound to SARS-CoV-2 spike
    • Complex: SARS-CoV-2 spike
    • Complex: N3-1 Fab
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsGoike J / Hsieh C-L / McLellan JS / Gollihar JD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI127521 United States
CitationJournal: To Be Published
Title: Discovery of potent SARS-CoV-2 neutralizing antibodies and a novel quaternary binding mode
Authors: Goike J / Hsieh C-L / McLellan JS / Gollihar JD
History
DepositionOct 15, 2021-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateNov 16, 2022-
Current statusNov 16, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25150.png

Downloads & links

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Map

FileDownload / File: emd_25150.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 432 pix.
= 475.2 Å		1.1 Å/pix.
x 432 pix.
= 475.2 Å		1.1 Å/pix.
x 432 pix.
= 475.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.56
Minimum - Maximum-3.6797853 - 8.710251
Average (Standard dev.)-0.0033236085 (±0.15173419)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 475.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_25150_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_25150_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 : Complex of N3-1 bound to SARS-CoV-2 spike

EntireName: Complex of N3-1 bound to SARS-CoV-2 spike
Components
  • Complex: Complex of N3-1 bound to SARS-CoV-2 spike
    • Complex: SARS-CoV-2 spike
    • Complex: N3-1 Fab

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Supramolecule #1: Complex of N3-1 bound to SARS-CoV-2 spike

SupramoleculeName: Complex of N3-1 bound to SARS-CoV-2 spike / type: complex / ID: 1 / Parent: 0

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Supramolecule #2: SARS-CoV-2 spike

SupramoleculeName: SARS-CoV-2 spike / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: N3-1 Fab

SupramoleculeName: N3-1 Fab / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: 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

Concentration0.2 mg/mL
BufferpH: 8 / Details: 2 mM Tris pH 7.5, 200 mM NaCl, 0.02% NaN3
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K
DetailsCollected on UltrAuFoil 1.2-1.3 with 0.2 mg/mL HexaPro (2 mM Tris pH 7.5, 200 mM NaCl, 0.02% NaN3) and 5x fold molar excess FabN3-1 spiked in 30 minutes before freezing.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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

6xkl

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 269553
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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