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- PDB-8erq: SARS-CoV-2 BA.1 spike ectodomain trimer in complex with the S2X32... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8erq | ||||||
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Title | SARS-CoV-2 BA.1 spike ectodomain trimer in complex with the S2X324 neutralizing antibody Fab fragment (local refinement of the RBD and S2X324) | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / COVID-19 / spike glycoprotein / fusion protein / neutralizing antibodies / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / inhibitor / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() 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 / entry receptor-mediated virion attachment to host cell ...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 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
![]() | Park, Y.J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Imprinted antibody responses against SARS-CoV-2 Omicron sublineages. Authors: Young-Jun Park / Dora Pinto / Alexandra C Walls / Zhuoming Liu / Anna De Marco / Fabio Benigni / Fabrizia Zatta / Chiara Silacci-Fregni / Jessica Bassi / Kaitlin R Sprouse / Amin Addetia / ...Authors: Young-Jun Park / Dora Pinto / Alexandra C Walls / Zhuoming Liu / Anna De Marco / Fabio Benigni / Fabrizia Zatta / Chiara Silacci-Fregni / Jessica Bassi / Kaitlin R Sprouse / Amin Addetia / John E Bowen / Cameron Stewart / Martina Giurdanella / Christian Saliba / Barbara Guarino / Michael A Schmid / Nicholas M Franko / Jennifer K Logue / Ha V Dang / Kevin Hauser / Julia di Iulio / William Rivera / Gretja Schnell / Anushka Rajesh / Jiayi Zhou / Nisar Farhat / Hannah Kaiser / Martin Montiel-Ruiz / Julia Noack / Florian A Lempp / Javier Janer / Rana Abdelnabi / Piet Maes / Paolo Ferrari / Alessandro Ceschi / Olivier Giannini / Guilherme Dias de Melo / Lauriane Kergoat / Hervé Bourhy / Johan Neyts / Leah Soriaga / Lisa A Purcell / Gyorgy Snell / Sean P J Whelan / Antonio Lanzavecchia / Herbert W Virgin / Luca Piccoli / Helen Y Chu / Matteo Samuele Pizzuto / Davide Corti / David Veesler / ![]() ![]() ![]() ![]() ![]() Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages carry distinct spike mutations resulting in escape from antibodies induced by previous infection or vaccination. We ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages carry distinct spike mutations resulting in escape from antibodies induced by previous infection or vaccination. We show that hybrid immunity or vaccine boosters elicit plasma-neutralizing antibodies against Omicron BA.1, BA.2, BA.2.12.1, and BA.4/5, and that breakthrough infections, but not vaccination alone, induce neutralizing antibodies in the nasal mucosa. Consistent with immunological imprinting, most antibodies derived from memory B cells or plasma cells of Omicron breakthrough cases cross-react with the Wuhan-Hu-1, BA.1, BA.2, and BA.4/5 receptor-binding domains, whereas Omicron primary infections elicit B cells of narrow specificity up to 6 months after infection. Although most clinical antibodies have reduced neutralization of Omicron, we identified an ultrapotent pan-variant-neutralizing antibody that is a strong candidate for clinical development. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112 KB | Display | ![]() |
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PDB format | ![]() | 73.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 29.7 KB | Display | |
Data in CIF | ![]() | 39.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 28558MC ![]() 8errC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Antibody | Mass: 13201.017 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 11513.587 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 141870.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Omicron BA.1 Spike glycoprotein,Omicron BA.1 Spike glycoprotein,Omicron BA.1 Spike glycoprotein,Omicron BA.1 Spike glycoprotein Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() |
#4: Sugar | ChemComp-NAG / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 354249 / Symmetry type: POINT |