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- EMDB-22860: SARS-CoV spike in complex with CR3022 Fab (3 Fab bound) -

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Basic information

Entry
Database: EMDB / ID: EMD-22860
TitleSARS-CoV spike in complex with CR3022 Fab (3 Fab bound)
Map dataRefined map
Sample
  • Complex: SARS-CoV spike in complex with CR3022 Fab (3 Fab bound)
Biological speciesSevere acute respiratory syndrome-related coronavirus
Methodsingle particle reconstruction / negative staining / Resolution: 24.0 Å
AuthorsWard AB / Bangaru S
Funding support United States, 2 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI110657 United States
CitationJournal: bioRxiv / Year: 2020
Title: A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody.
Authors: Nicholas C Wu / Meng Yuan / Sandhya Bangaru / Deli Huang / Xueyong Zhu / Chang-Chun D Lee / Hannah L Turner / Linghang Peng / Linlin Yang / David Nemazee / Andrew B Ward / Ian A Wilson /
Abstract: Epitopes that are conserved among SARS-like coronaviruses are attractive targets for design of cross-reactive vaccines and therapeutics. CR3022 is a SARS-CoV neutralizing antibody to a highly ...Epitopes that are conserved among SARS-like coronaviruses are attractive targets for design of cross-reactive vaccines and therapeutics. CR3022 is a SARS-CoV neutralizing antibody to a highly conserved epitope on the receptor binding domain (RBD) on the spike protein that can cross-react with SARS-CoV-2, but with lower affinity. Using x-ray crystallography, mutagenesis, and binding experiments, we illustrate that of four amino acid differences in the CR3022 epitope between SARS-CoV-2 and SARS-CoV, a single mutation P384A fully determines the affinity difference. CR3022 does not neutralize SARS-CoV-2, but the increased affinity to SARS-CoV-2 P384A mutant now enables neutralization with a similar potency to SARS-CoV. We further investigated CR3022 interaction with the SARS-CoV spike protein by negative-stain EM and cryo-EM. Three CR3022 Fabs bind per trimer with the RBD observed in different up-conformations due to considerable flexibility of the RBD. In one of these conformations, quaternary interactions are made by CR3022 to the N-terminal domain (NTD) of an adjacent subunit. Overall, this study provides insights into antigenic variation and potential for cross-neutralizing epitopes on SARS-like viruses.
History
DepositionOct 15, 2020-
Header (metadata) releaseOct 28, 2020-
Map releaseOct 28, 2020-
UpdateOct 28, 2020-
Current statusOct 28, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22860.png

Downloads & links

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Map

FileDownload / File: emd_22860.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefined map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 256 pix.
= 527.36 Å		2.06 Å/pix.
x 256 pix.
= 527.36 Å		2.06 Å/pix.
x 256 pix.
= 527.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019 / Movie #1: 0.019
Minimum - Maximum-0.042297963 - 0.07349298
Average (Standard dev.)-0.00022570783 (±0.0027118432)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 527.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.062.062.06
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z527.360527.360527.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0420.073-0.000

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Supplemental data

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Sample components

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Entire : SARS-CoV spike in complex with CR3022 Fab (3 Fab bound)

EntireName: SARS-CoV spike in complex with CR3022 Fab (3 Fab bound)
Components
  • Complex: SARS-CoV spike in complex with CR3022 Fab (3 Fab bound)

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Supramolecule #1: SARS-CoV spike in complex with CR3022 Fab (3 Fab bound)

SupramoleculeName: SARS-CoV spike in complex with CR3022 Fab (3 Fab bound)
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome-related coronavirus
Recombinant expressionOrganism: Homo sapiens (human)

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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

Concentration0.02 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Formate
GridMaterial: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 6331
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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