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- EMDB-44644: SARS CoV2 spike in complex with NTD-directed antibody Fab DH1052 -

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Basic information

Entry
Database: EMDB / ID: EMD-44644
TitleSARS CoV2 spike in complex with NTD-directed antibody Fab DH1052
Map dataCoV2 spike in complex with antibody Fab DH1052
Sample
  • Complex: Complex of SARS CoV2 spike with NTD-directed antibody Fab DH1052
    • Complex: DH1052 antibody Fab
    • Complex: SARS CoV2 spike
KeywordsSARS coronavirus spike antibody / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 15.0 Å
AuthorsEdwards RJ / Mansouri K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI158571 United States
CitationJournal: PLoS Pathog.
Title: Non-neutralizing SARS-CoV-2 N-terminal domain antibodies protects mice against severe disease using Fc effector functions
Authors: Pierre CN / Adams LE / Anasti K / Goodman D / Stanfield-Oakley S / Li D / Rountree W / Wang Y / Edwards RJ / Alam SM / Ferrari G / Tomaras GD / Haynes BF / Baric RS / Saunders KO
History
DepositionApr 29, 2024-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44644.png

Downloads & links

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Map

FileDownload / File: emd_44644.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCoV2 spike in complex with antibody Fab DH1052
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.74 Å/pix.
x 96 pix.
= 359.04 Å		3.74 Å/pix.
x 96 pix.
= 359.04 Å		3.74 Å/pix.
x 96 pix.
= 359.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.078417115 - 0.15856627
Average (Standard dev.)0.00054337183 (±0.0118801035)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 359.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_44644_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_44644_half_map_2.map
AnnotationHalf map 2
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 SARS CoV2 spike with NTD-directed antibody Fab DH1052

EntireName: Complex of SARS CoV2 spike with NTD-directed antibody Fab DH1052
Components
  • Complex: Complex of SARS CoV2 spike with NTD-directed antibody Fab DH1052
    • Complex: DH1052 antibody Fab
    • Complex: SARS CoV2 spike

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Supramolecule #1: Complex of SARS CoV2 spike with NTD-directed antibody Fab DH1052

SupramoleculeName: Complex of SARS CoV2 spike with NTD-directed antibody Fab DH1052
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 372 KDa

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Supramolecule #2: DH1052 antibody Fab

SupramoleculeName: DH1052 antibody Fab / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: SARS CoV2 spike

SupramoleculeName: SARS CoV2 spike / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
20.0 mMHEPESHEPES buffer
StainingType: NEGATIVE / Material: Uranyl formate
Details: A 5 microliter drop of complex was incubated on the grid for 10 to 15 s, blotted and then stained with 2 percent uranyl formate for 1 minute, then blotted and air dried.
GridModel: Homemade / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
DetailsSpike protein and Fab protein at 1 mg per ml were stored at minus 80 degrees C until use. Spike was thawed in an aluminum block at 37 degrees C for 5 minutes, Fab was thawed in an aluminum block at room temperature for 5 minutes. To for the complex, 2 microliters of spike was mixed with Fab at a 1 to 9 ratio spike to Fab, and incubated at 37 degrees C for 1 hour. The complex was then crosslinked by diluting to a final spike concentration of 0.1 mg per ml into room temperature buffer containing 150 mM NaCl, 20 mM HEPES pH 7.4, 5 percent glycerol, and 7.5 mM glutaraldehyde. After 5 minutes cross-linking, excess glutaraldehyde was quenched by adding sufficient 1 M Tris pH 7.4 stock to give a final concentration of 75 mM Tris and incubated for 5 minutes.

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Electron microscopy

MicroscopeFEI/PHILIPS EM420
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 82000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Image recordingFilm or detector model: OTHER / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number grids imaged: 1 / Number real images: 200 / Average exposure time: 0.5 sec. / Average electron dose: 32.0 e/Å2

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Image processing

Particle selectionNumber selected: 154496
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7vsb


Details: starting model was bare spike model, no Fabs, low pass filtered to 30 angstroms.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 10733 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: EXACT BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 11845
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7vsb


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: cross correlation

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