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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 / Year: 2024
Title: Non-neutralizing SARS-CoV-2 N-terminal domain antibodies protect mice against severe disease using Fc-mediated effector functions.
Authors: Camille N Pierre / Lily E Adams / Jaclyn S Higgins / Kara Anasti / Derrick Goodman / Dieter Mielke / Sherry Stanfield-Oakley / John M Powers / Dapeng Li / Wes Rountree / Yunfei Wang / Robert ...Authors: Camille N Pierre / Lily E Adams / Jaclyn S Higgins / Kara Anasti / Derrick Goodman / Dieter Mielke / Sherry Stanfield-Oakley / John M Powers / Dapeng Li / Wes Rountree / Yunfei Wang / Robert J Edwards / S Munir Alam / Guido Ferrari / Georgia D Tomaras / Barton F Haynes / Ralph S Baric / Kevin O Saunders /
Abstract: Antibodies perform both neutralizing and non-neutralizing effector functions that protect against certain pathogen-induced diseases. A human antibody directed at the SARS-CoV-2 Spike N-terminal ...Antibodies perform both neutralizing and non-neutralizing effector functions that protect against certain pathogen-induced diseases. A human antibody directed at the SARS-CoV-2 Spike N-terminal domain (NTD), DH1052, was recently shown to be non-neutralizing, yet it protected mice and cynomolgus macaques from severe disease. The mechanisms of NTD non-neutralizing antibody-mediated protection are unknown. Here we show that Fc effector functions mediate NTD non-neutralizing antibody (non-nAb) protection against SARS-CoV-2 MA10 viral challenge in mice. Though non-nAb prophylactic infusion did not suppress infectious viral titers in the lung as potently as neutralizing antibody (nAb) infusion, disease markers including gross lung discoloration were similar in nAb and non-nAb groups. Fc functional knockout substitutions abolished non-nAb protection and increased viral titers in the nAb group. Fc enhancement increased non-nAb protection relative to WT, supporting a positive association between Fc functionality and degree of protection from SARS-CoV-2 infection. For therapeutic administration of antibodies, non-nAb effector functions contributed to virus suppression and lessening of lung discoloration, but the presence of neutralization was required for optimal protection from disease. This study demonstrates that non-nAbs can utilize Fc-mediated mechanisms to lower viral load and prevent lung damage due to coronavirus infection.
History
DepositionApr 29, 2024-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateJul 3, 2024-
Current statusJul 3, 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 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
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
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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

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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.
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
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 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)
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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