Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	The presence of broadly neutralizing anti-SARS-CoV-2 RBD antibodies elicited by primary series and booster dose of COVID-19 vaccine.
Journal, issue, pages	PLoS Pathog, Vol. 20, Issue 6, Page e1012246, Year 2024
Publish date	Jun 10, 2024
Authors	Xiaorui Chen / Arpita Mohapatra / Hong Thuy Vy Nguyen / Lisa Schimanski / Tiong Kit Tan / Pramila Rijal / Cheng-Pin Chen / Shu-Hsing Cheng / Wen-Hsin Lee / Yu-Chi Chou / Alain R Townsend / Che Ma / Kuan-Ying A Huang /
PubMed Abstract	Antibody-mediated immunity plays a key role in protection against SARS-CoV-2. We characterized B-cell-derived anti-SARS-CoV-2 RBD antibody repertoires from vaccinated and infected individuals and ...Antibody-mediated immunity plays a key role in protection against SARS-CoV-2. We characterized B-cell-derived anti-SARS-CoV-2 RBD antibody repertoires from vaccinated and infected individuals and elucidate the mechanism of action of broadly neutralizing antibodies and dissect antibodies at the epitope level. The breadth and clonality of anti-RBD B cell response varies among individuals. The majority of neutralizing antibody clones lose or exhibit reduced activities against Beta, Delta, and Omicron variants. Nevertheless, a portion of anti-RBD antibody clones that develops after a primary series or booster dose of COVID-19 vaccination exhibit broad neutralization against emerging Omicron BA.2, BA.4, BA.5, BQ.1.1, XBB.1.5 and XBB.1.16 variants. These broadly neutralizing antibodies share genetic features including a conserved usage of the IGHV3-53 and 3-9 genes and recognize three clustered epitopes of the RBD, including epitopes that partially overlap the classically defined set identified early in the pandemic. The Fab-RBD crystal and Fab-Spike complex structures corroborate the epitope grouping of antibodies and reveal the detailed binding mode of broadly neutralizing antibodies. Structure-guided mutagenesis improves binding and neutralization potency of antibody with Omicron variants via a single amino-substitution. Together, these results provide an immunological basis for partial protection against severe COVID-19 by the ancestral strain-based vaccine and indicate guidance for next generation monoclonal antibody development and vaccine design.
External links	PLoS Pathog / PubMed:38857264 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.94 - 4.55 Å
Structure data	39546 8yro EMDB-39546, PDB-8yro: SARS-CoV-2 Delta Spike in complex with JL-8C Method: EM (single particle) / Resolution: 3.27 Å 39547 8yrp EMDB-39547, PDB-8yrp: SARS-CoV-2 Delta Spike in complex with JM-1A Method: EM (single particle) / Resolution: 3.64 Å 39685 8yz5 EMDB-39685, PDB-8yz5: SARS-CoV-2 Delta Spike in complex with Fab of JE-5C Method: EM (single particle) / Resolution: 3.93 Å 39686 8yz6 EMDB-39686, PDB-8yz6: SARS-CoV-2 Spike (BA.1) in complex with Fab of JH-8B Method: EM (single particle) / Resolution: 4.55 Å PDB-8x0x: Crystal structure of JE-5C in complex with SARS-CoV-2 RBD Method: X-RAY DIFFRACTION / Resolution: 3.45 Å PDB-8x0y: Crystal structure of JM-1A in complex with SARS-CoV-2 RBD Method: X-RAY DIFFRACTION / Resolution: 1.94 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose ChemComp-SO4: SULFATE ION ChemComp-HOH: WATER ChemComp-CL: Unknown entry ChemComp-PO4: PHOSPHATE ION
Source	severe acute respiratory syndrome coronavirus 2 homo sapiens (human)
Keywords	VIRAL PROTEIN/IMMUNE SYSTEM / Antibody / broad neutralization / class 1/2 / Omicron variants / vaccine / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex / 3-up