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- EMDB-22627: Negative stain EM map of SARS-COV-2 spike protein (trimer) with F... -

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Basic information

Entry
Database: EMDB / ID: EMD-22627
TitleNegative stain EM map of SARS-COV-2 spike protein (trimer) with Fab COV2-2082
Map data
Sample
  • Complex: SARS-COV-2 spike protein (trimer) with Fab COV2-2082
    • Complex: SARS-COV-2 spike protein (trimer)
    • Complex: Fab COV2-2082
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 28.0 Å
AuthorsBinshtein E / Crowe JE
Funding support United States, 2 items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)HR0011-18-2-0001 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00074 United States
CitationJournal: Cell Host Microbe / Year: 2021
Title: Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition.
Authors: Allison J Greaney / Tyler N Starr / Pavlo Gilchuk / Seth J Zost / Elad Binshtein / Andrea N Loes / Sarah K Hilton / John Huddleston / Rachel Eguia / Katharine H D Crawford / Adam S Dingens / ...Authors: Allison J Greaney / Tyler N Starr / Pavlo Gilchuk / Seth J Zost / Elad Binshtein / Andrea N Loes / Sarah K Hilton / John Huddleston / Rachel Eguia / Katharine H D Crawford / Adam S Dingens / Rachel S Nargi / Rachel E Sutton / Naveenchandra Suryadevara / Paul W Rothlauf / Zhuoming Liu / Sean P J Whelan / Robert H Carnahan / James E Crowe / Jesse D Bloom /
Abstract: Antibodies targeting the SARS-CoV-2 spike receptor-binding domain (RBD) are being developed as therapeutics and are a major contributor to neutralizing antibody responses elicited by infection. Here, ...Antibodies targeting the SARS-CoV-2 spike receptor-binding domain (RBD) are being developed as therapeutics and are a major contributor to neutralizing antibody responses elicited by infection. Here, we describe a deep mutational scanning method to map how all amino-acid mutations in the RBD affect antibody binding and apply this method to 10 human monoclonal antibodies. The escape mutations cluster on several surfaces of the RBD that broadly correspond to structurally defined antibody epitopes. However, even antibodies targeting the same surface often have distinct escape mutations. The complete escape maps predict which mutations are selected during viral growth in the presence of single antibodies. They further enable the design of escape-resistant antibody cocktails-including cocktails of antibodies that compete for binding to the same RBD surface but have different escape mutations. Therefore, complete escape-mutation maps enable rational design of antibody therapeutics and assessment of the antigenic consequences of viral evolution.
History
DepositionSep 8, 2020-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 2020-
UpdateJan 27, 2021-
Current statusJan 27, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22627.png

Downloads & links

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Map

FileDownload / File: emd_22627.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.36 Å/pix.
x 128 pix.
= 558.08 Å		4.36 Å/pix.
x 128 pix.
= 558.08 Å		4.36 Å/pix.
x 128 pix.
= 558.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0 / Movie #1: 5
Minimum - Maximum-7.6184554 - 28.394384
Average (Standard dev.)-0.28018662 (±1.1072897)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 558.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.364.364.36
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z558.080558.080558.080
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-7.61828.394-0.280

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Supplemental data

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Sample components

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Entire : SARS-COV-2 spike protein (trimer) with Fab COV2-2082

EntireName: SARS-COV-2 spike protein (trimer) with Fab COV2-2082
Components
  • Complex: SARS-COV-2 spike protein (trimer) with Fab COV2-2082
    • Complex: SARS-COV-2 spike protein (trimer)
    • Complex: Fab COV2-2082

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Supramolecule #1: SARS-COV-2 spike protein (trimer) with Fab COV2-2082

SupramoleculeName: SARS-COV-2 spike protein (trimer) with Fab COV2-2082 / type: complex / ID: 1 / Parent: 0

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Supramolecule #2: SARS-COV-2 spike protein (trimer)

SupramoleculeName: SARS-COV-2 spike protein (trimer) / 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: Fab COV2-2082

SupramoleculeName: Fab COV2-2082 / 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

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
2.0 mMTris
200.0 mMsodium chlorideNaCl
StainingType: NEGATIVE / Material: UF
GridMaterial: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number grids imaged: 1 / Number real images: 237 / Average exposure time: 1.0 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 1.9 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 972
CTF correctionSoftware - Name: cryoSPARC (ver. 2.15)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 673
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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