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	Mapping cross-variant neutralizing sites on the SARS-CoV-2 spike protein.
Journal, issue, pages	Emerg Microbes Infect, Vol. 11, Issue 1, Page 351-367, Year 2022
Publish date	Jan 27, 2022
Authors	Shiqi Xu / Yifan Wang / Yanxing Wang / Chao Zhang / Qin Hong / Chenjian Gu / Rong Xu / Tingfeng Wang / Yong Yang / Jinkai Zang / Yu Zhou / Zuyang Li / Qixing Liu / Bingjie Zhou / Lulu Bai / Yuanfei Zhu / Qiang Deng / Haikun Wang / Dimitri Lavillette / Gary Wong / Youhua Xie / Yao Cong / Zhong Huang /
PubMed Abstract	The emergence of multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern threatens the efficacy of currently approved vaccines and authorized therapeutic monoclonal ...The emergence of multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern threatens the efficacy of currently approved vaccines and authorized therapeutic monoclonal antibodies (MAbs). It is hence important to continue searching for SARS-CoV-2 broadly neutralizing MAbs and defining their epitopes. Here, we isolate 9 neutralizing mouse MAbs raised against the spike protein of a SARS-CoV-2 prototype strain and evaluate their neutralizing potency towards a panel of variants, including B.1.1.7, B.1.351, B.1.617.1, and B.1.617.2. By using a combination of biochemical, virological, and cryo-EM structural analyses, we identify three types of cross-variant neutralizing MAbs, represented by S5D2, S5G2, and S3H3, respectively, and further define their epitopes. S5D2 binds the top lateral edge of the receptor-binding motif within the receptor-binding domain (RBD) with a binding footprint centred around the loop, and efficiently neutralizes all variant pseudoviruses, but the potency against B.1.617.2 was observed to decrease significantly. S5G2 targets the highly conserved RBD core region and exhibits comparable neutralization towards the variant panel. S3H3 binds a previously unreported epitope located within the evolutionarily stable SD1 region and is able to near equally neutralize all of the variants tested. Our work thus defines three distinct cross-variant neutralizing sites on the SARS-CoV-2 spike protein, providing guidance for design and development of broadly effective vaccines and MAb-based therapies.
External links	Emerg Microbes Infect / PubMed:34964428 / PubMed Central
Methods	EM (single particle)
Resolution	3.3 - 4.3 Å
Structure data	32428 7wcr EMDB-32428, PDB-7wcr: RBD-1 of SARS-CoV-2 Beta spike in complex with S5D2 Fab Method: EM (single particle) / Resolution: 3.5 Å 32430 7wcz EMDB-32430, PDB-7wcz: SARS-CoV-2 Beta spike in complex with one S5D2 Fab Method: EM (single particle) / Resolution: 3.5 Å 32431 7wd0 EMDB-32431, PDB-7wd0: SARS-CoV-2 Beta spike in complex with two S5D2 Fabs Method: EM (single particle) / Resolution: 3.3 Å 32433 7wd7 EMDB-32433, PDB-7wd7: SARS-CoV-2 Beta spike in complex with three S5D2 Fabs Method: EM (single particle) / Resolution: 3.5 Å 32434 7wd8 EMDB-32434, PDB-7wd8: SARS-CoV-2 Beta spike SD1 in complex with S3H3 Fab Method: EM (single particle) / Resolution: 4.3 Å 32435 7wd9 EMDB-32435, PDB-7wd9: SARS-CoV-2 Beta spike in complex with three S3H3 Fabs Method: EM (single particle) / Resolution: 3.7 Å 32437 7wdf EMDB-32437, PDB-7wdf: SARS-CoV-2 Beta spike in complex with two S3H3 Fabs Method: EM (single particle) / Resolution: 3.9 Å
Source	severe acute respiratory syndrome coronavirus 2 mus musculus (house mouse)
Keywords	VIRAL PROTEIN / SARS-CoV-2 / coronavirus / Beta variant / B.1.351 lineage / spike protein