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- EMDB-23160: Prefusion-stabilized SARS-CoV-2 spike bound by the engineered hum... -

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Basic information

Entry
Database: EMDB / ID: EMD-23160
TitlePrefusion-stabilized SARS-CoV-2 spike bound by the engineered human antibody ADG-2
Map data
SamplePrefusion-stabilized SARS-CoV-2 spike bound by a single copy of ADG-2 Fab:
ADG-2 Fab / spike glycoproteinPeplomer
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 5.94 Å
AuthorsWrapp D / McLellan JS
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: Science / Year: 2021
Title: Broad and potent activity against SARS-like viruses by an engineered human monoclonal antibody.
Authors: C Garrett Rappazzo / Longping V Tse / Chengzi I Kaku / Daniel Wrapp / Mrunal Sakharkar / Deli Huang / Laura M Deveau / Thomas J Yockachonis / Andrew S Herbert / Michael B Battles / Cecilia M ...Authors: C Garrett Rappazzo / Longping V Tse / Chengzi I Kaku / Daniel Wrapp / Mrunal Sakharkar / Deli Huang / Laura M Deveau / Thomas J Yockachonis / Andrew S Herbert / Michael B Battles / Cecilia M O'Brien / Michael E Brown / James C Geoghegan / Jonathan Belk / Linghang Peng / Linlin Yang / Yixuan Hou / Trevor D Scobey / Dennis R Burton / David Nemazee / John M Dye / James E Voss / Bronwyn M Gunn / Jason S McLellan / Ralph S Baric / Lisa E Gralinski / Laura M Walker /
Abstract: The recurrent zoonotic spillover of coronaviruses (CoVs) into the human population underscores the need for broadly active countermeasures. We employed a directed evolution approach to engineer three ...The recurrent zoonotic spillover of coronaviruses (CoVs) into the human population underscores the need for broadly active countermeasures. We employed a directed evolution approach to engineer three severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies for enhanced neutralization breadth and potency. One of the affinity-matured variants, ADG-2, displays strong binding activity to a large panel of sarbecovirus receptor binding domains and neutralizes representative epidemic sarbecoviruses with high potency. Structural and biochemical studies demonstrate that ADG-2 employs a distinct angle of approach to recognize a highly conserved epitope that overlaps the receptor binding site. In immunocompetent mouse models of SARS and COVID-19, prophylactic administration of ADG-2 provided complete protection against respiratory burden, viral replication in the lungs, and lung pathology. Altogether, ADG-2 represents a promising broad-spectrum therapeutic candidate against clade 1 sarbecoviruses.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionDec 19, 2020-
Header (metadata) releaseFeb 10, 2021-
Map releaseFeb 10, 2021-
UpdateMar 3, 2021-
Current statusMar 3, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_23160.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 440 pix.
= 460.68 Å
1.05 Å/pix.
x 440 pix.
= 460.68 Å
1.05 Å/pix.
x 440 pix.
= 460.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.047 Å
Density
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.23477893 - 0.7339134
Average (Standard dev.)-0.00018431946 (±0.017313238)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 460.68002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0471.0471.047
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z460.680460.680460.680
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.2350.734-0.000

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Supplemental data

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Half map: Half map A

Fileemd_23160_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map B

Fileemd_23160_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Prefusion-stabilized SARS-CoV-2 spike bound by a single copy of A...

EntireName: Prefusion-stabilized SARS-CoV-2 spike bound by a single copy of ADG-2 Fab
Number of components: 3

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Component #1: protein, Prefusion-stabilized SARS-CoV-2 spike bound by a single ...

ProteinName: Prefusion-stabilized SARS-CoV-2 spike bound by a single copy of ADG-2 Fab
Recombinant expression: No
MassTheoretical: 500 kDa

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Component #2: protein, ADG-2 Fab

ProteinName: ADG-2 Fab / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, spike glycoprotein

ProteinName: spike glycoproteinPeplomer / Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: unidentified (others)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.35 mg/mL / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 278 K / Humidity: 100 % / Details: Blotted for 6 seconds at -1 force.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 36 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 57078
3D reconstructionSoftware: cryoSPARC / Resolution: 5.94 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Input PDB model: 6XKL

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