Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cryo-EM SPA datasets for Antibodies 12-16 & 12-19 in complex with prefusion SARS-CoV-2 Spike glycoprotein (K3 movies/.tif files)

ABSTRACT:

SUBMITTER: Ryan Gavin Casner

PROVIDER: EMPIAR-11335 | biostudies-other |

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

Antibodies targeting a quaternary site on SARS-CoV-2 spike glycoprotein prevent viral receptor engagement by conformational locking.

Liu Lihong L Casner Ryan G RG Guo Yicheng Y Wang Qian Q Iketani Sho S Chan Jasper Fuk-Woo JF Yu Jian J Dadonaite Bernadeta B Nair Manoj S MS Mohri Hiroshi H Reddem Eswar R ER Yuan Shuofeng S Poon Vincent Kwok-Man VK Chan Chris Chung-Sing CC Yuen Kwok-Yung KY Sheng Zizhang Z Huang Yaoxing Y Bloom Jesse D JD Shapiro Lawrence L Ho David D DD

Immunity 20230929 10

SARS-CoV-2 continues to evolve, with many variants evading clinically authorized antibodies. To isolate monoclonal antibodies (mAbs) with broadly neutralizing capacities against the virus, we screened serum samples from convalescing COVID-19 patients. We isolated two mAbs, 12-16 and 12-19, which neutralized all SARS-CoV-2 variants tested, including the XBB subvariants, and prevented infection in hamsters challenged with Omicron BA.1 intranasally. Structurally, both antibodies targeted a conserve ...[more]

PMID: 37776849

Similar Datasets

Cryo-EM SPA datasets for Antibody 4-33 in complex with prefusion SARS-CoV-2 Spike glycoprotein (K3 movies/.tif files)

Project description: Not available

| EMPIAR-11336 | biostudies-other

Cryo-EM SPA datasets of broadly neutralizing antibody 2-36 in complex with prefusion SARS-CoV-2 and SARS-CoV spike glycoproteins (K3 movies/.tif files)

Project description: Not available

| EMPIAR-11513 | biostudies-other

Cryo-EM SPA dataset for Antibody SKV09 in complex with VEEV VLP (K3 movies/.tif files)

Project description: Not available

| EMPIAR-11338 | biostudies-other

Architecture of the SARS coronavirus prefusion spike.

Project description:The emergence in 2003 of a new coronavirus (CoV) responsible for the atypical pneumonia termed severe acute respiratory syndrome (SARS) was a stark reminder that hitherto unknown viruses have the potential to cross species barriers to become new human pathogens. Here we describe the SARS-CoV 'spike' structure determined by single-particle cryo-EM, along with the docked atomic structures of the receptor-binding domain and prefusion core.

| S-EPMC7097490 | biostudies-literature

Cryo electron microscopy of SARS-CoV-2 spike in prefusion state

Project description: Not available

| EMPIAR-10516 | biostudies-other

Cryo electron microscopy of SARS-CoV-2 stabilized spike in prefusion state

Project description: Not available

| EMPIAR-10514 | biostudies-other

Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures.

Project description:Using a new consensus-based image-processing approach together with principal component analysis, the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state have been analysed. These studies revealed concerted motions involving the receptor-binding domain (RBD), N-terminal domain, and subdomains 1 and 2 around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. It is shown that in this data set there are not well defined, stable spike conformations, but virtually a continuum of states. An ensemble map was obtained with minimum bias, from which the extremes of the change along the direction of maximal variance were modeled by flexible fitting. The results provide a warning of the potential image-processing classification instability of these complicated data sets, which has a direct impact on the interpretability of the results.

| S-EPMC7553147 | biostudies-literature

Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures.

Project description:With the help of novel processing workflows and algorithms, we have obtained a better understanding of the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state. We have re-analyzed previous cryo-EM data combining 3D clustering approaches with ways to explore a continuous flexibility space based on 3D Principal Component Analysis. These advanced analyses revealed a concerted motion involving the receptor-binding domain (RBD), N-terminal domain (NTD), and subdomain 1 and 2 (SD1 & SD2) around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. We show that in this dataset there are not well-defined, stable, spike conformations, but virtually a continuum of states moving in a concerted fashion. We obtained an improved resolution ensemble map with minimum bias, from which we model by flexible fitting the extremes of the change along the direction of maximal variance. Moreover, a high-resolution structure of a recently described biochemically stabilized form of the spike is shown to greatly reduce the dynamics observed for the wild-type spike. Our results provide new detailed avenues to potentially restrain the spike dynamics for structure-based drug and vaccine design and at the same time give a warning of the potential image processing classification instability of these complicated datasets, having a direct impact on the interpretability of the results.

| S-EPMC7359526 | biostudies-literature

Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike.

Project description:There are as yet no licensed therapeutics for the COVID-19 pandemic. The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric spike whose receptor binding domain (RBD) recognizes angiotensin-converting enzyme 2, initiating conformational changes that drive membrane fusion. We find that the monoclonal antibody CR3022 binds the RBD tightly, neutralizing SARS-CoV-2, and report the crystal structure at 2.4 Å of the Fab/RBD complex. Some crystals are suitable for screening for entry-blocking inhibitors. The highly conserved, structure-stabilizing CR3022 epitope is inaccessible in the prefusion spike, suggesting that CR3022 binding facilitates conversion to the fusion-incompetent post-fusion state. Cryogenic electron microscopy (cryo-EM) analysis confirms that incubation of spike with CR3022 Fab leads to destruction of the prefusion trimer. Presentation of this cryptic epitope in an RBD-based vaccine might advantageously focus immune responses. Binders at this epitope could be useful therapeutically, possibly in synergy with an antibody that blocks receptor attachment.

| S-EPMC7303615 | biostudies-literature

Single-particle cryo-EM unaligned micrographs of prefusion SARS-CoV-2 spike omicron B.1.1.529 variant

Project description: Not available

| EMPIAR-11871 | biostudies-other