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- EMDB-24357: Negative stain EM map of SARS-CoV-2 Spike in complex with CoVIC-0... -

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Basic information

Entry
Database: EMDB / ID: EMD-24357
TitleNegative stain EM map of SARS-CoV-2 Spike in complex with CoVIC-090 IgG
Map dataNegative stain EM map of SARS-CoV-2 Spike in complex with CoVIC-090 IgG
Sample
  • Complex: The complex of SARS-CoV-2 Spike and CoVIC-090 IgG
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / negative staining / Resolution: 21.0 Å
AuthorsSaphire EO / Hui S
Funding support United States, 3 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-006133 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5U19AI142790 United States
Other privateGHR Foundation
CitationJournal: Science / Year: 2021
Title: Defining variant-resistant epitopes targeted by SARS-CoV-2 antibodies: A global consortium study.
Authors: Kathryn M Hastie / Haoyang Li / Daniel Bedinger / Sharon L Schendel / S Moses Dennison / Kan Li / Vamseedhar Rayaprolu / Xiaoying Yu / Colin Mann / Michelle Zandonatti / Ruben Diaz Avalos / ...Authors: Kathryn M Hastie / Haoyang Li / Daniel Bedinger / Sharon L Schendel / S Moses Dennison / Kan Li / Vamseedhar Rayaprolu / Xiaoying Yu / Colin Mann / Michelle Zandonatti / Ruben Diaz Avalos / Dawid Zyla / Tierra Buck / Sean Hui / Kelly Shaffer / Chitra Hariharan / Jieyun Yin / Eduardo Olmedillas / Adrian Enriquez / Diptiben Parekh / Milite Abraha / Elizabeth Feeney / Gillian Q Horn / / Yoann Aldon / Hanif Ali / Sanja Aracic / Ronald R Cobb / Ross S Federman / Joseph M Fernandez / Jacob Glanville / Robin Green / Gevorg Grigoryan / Ana G Lujan Hernandez / David D Ho / Kuan-Ying A Huang / John Ingraham / Weidong Jiang / Paul Kellam / Cheolmin Kim / Minsoo Kim / Hyeong Mi Kim / Chao Kong / Shelly J Krebs / Fei Lan / Guojun Lang / Sooyoung Lee / Cheuk Lun Leung / Junli Liu / Yanan Lu / Anna MacCamy / Andrew T McGuire / Anne L Palser / Terence H Rabbitts / Zahra Rikhtegaran Tehrani / Mohammad M Sajadi / Rogier W Sanders / Aaron K Sato / Liang Schweizer / Jimin Seo / Bingqing Shen / Jonne L Snitselaar / Leonidas Stamatatos / Yongcong Tan / Milan T Tomic / Marit J van Gils / Sawsan Youssef / Jian Yu / Tom Z Yuan / Qian Zhang / Bjoern Peters / Georgia D Tomaras / Timothy Germann / Erica Ollmann Saphire /
Abstract: Antibody-based therapeutics and vaccines are essential to combat COVID-19 morbidity and mortality after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Multiple mutations in ...Antibody-based therapeutics and vaccines are essential to combat COVID-19 morbidity and mortality after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Multiple mutations in SARS-CoV-2 that could impair antibody defenses propagated in human-to-human transmission and spillover or spillback events between humans and animals. To develop prevention and therapeutic strategies, we formed an international consortium to map the epitope landscape on the SARS-CoV-2 spike protein, defining and structurally illustrating seven receptor binding domain (RBD)–directed antibody communities with distinct footprints and competition profiles. Pseudovirion-based neutralization assays reveal spike mutations, individually and clustered together in variants, that affect antibody function among the communities. Key classes of RBD-targeted antibodies maintain neutralization activity against these emerging SARS-CoV-2 variants. These results provide a framework for selecting antibody treatment cocktails and understanding how viral variants might affect antibody therapeutic efficacy.
History
DepositionJun 30, 2021-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 2021-
UpdateNov 3, 2021-
Current statusNov 3, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24357.png

Downloads & links

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Map

FileDownload / File: emd_24357.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain EM map of SARS-CoV-2 Spike in complex with CoVIC-090 IgG
Voxel sizeX=Y=Z: 5.4 Å
Density
Contour LevelBy AUTHOR: 4.5 / Movie #1: 4.5
Minimum - Maximum-4.4221096 - 18.3916
Average (Standard dev.)-0.033933256 (±0.5958337)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 691.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.45.45.4
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z691.200691.200691.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-4.42218.392-0.034

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Supplemental data

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Sample components

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Entire : The complex of SARS-CoV-2 Spike and CoVIC-090 IgG

EntireName: The complex of SARS-CoV-2 Spike and CoVIC-090 IgG
Components
  • Complex: The complex of SARS-CoV-2 Spike and CoVIC-090 IgG

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Supramolecule #1: The complex of SARS-CoV-2 Spike and CoVIC-090 IgG

SupramoleculeName: The complex of SARS-CoV-2 Spike and CoVIC-090 IgG / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)

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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

BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Formate

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Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2

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Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23551

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