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	BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection.
Journal, issue, pages	Nature, Vol. 608, Issue 7923, Page 593-602, Year 2022
Publish date	Jun 17, 2022
Authors	Yunlong Cao / Ayijiang Yisimayi / Fanchong Jian / Weiliang Song / Tianhe Xiao / Lei Wang / Shuo Du / Jing Wang / Qianqian Li / Xiaosu Chen / Yuanling Yu / Peng Wang / Zhiying Zhang / Pulan Liu / Ran An / Xiaohua Hao / Yao Wang / Jing Wang / Rui Feng / Haiyan Sun / Lijuan Zhao / Wen Zhang / Dong Zhao / Jiang Zheng / Lingling Yu / Can Li / Na Zhang / Rui Wang / Xiao Niu / Sijie Yang / Xuetao Song / Yangyang Chai / Ye Hu / Yansong Shi / Linlin Zheng / Zhiqiang Li / Qingqing Gu / Fei Shao / Weijin Huang / Ronghua Jin / Zhongyang Shen / Youchun Wang / Xiangxi Wang / Junyu Xiao / Xiaoliang Sunney Xie /
PubMed Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages BA.2.12.1, BA.4 and BA.5 exhibit higher transmissibility than the BA.2 lineage. The receptor binding and immune- ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages BA.2.12.1, BA.4 and BA.5 exhibit higher transmissibility than the BA.2 lineage. The receptor binding and immune-evasion capability of these recently emerged variants require immediate investigation. Here, coupled with structural comparisons of the spike proteins, we show that BA.2.12.1, BA.4 and BA.5 (BA.4 and BA.5 are hereafter referred collectively to as BA.4/BA.5) exhibit similar binding affinities to BA.2 for the angiotensin-converting enzyme 2 (ACE2) receptor. Of note, BA.2.12.1 and BA.4/BA.5 display increased evasion of neutralizing antibodies compared with BA.2 against plasma from triple-vaccinated individuals or from individuals who developed a BA.1 infection after vaccination. To delineate the underlying antibody-evasion mechanism, we determined the escape mutation profiles, epitope distribution and Omicron-neutralization efficiency of 1,640 neutralizing antibodies directed against the receptor-binding domain of the viral spike protein, including 614 antibodies isolated from people who had recovered from BA.1 infection. BA.1 infection after vaccination predominantly recalls humoral immune memory directed against ancestral (hereafter referred to as wild-type (WT)) SARS-CoV-2 spike protein. The resulting elicited antibodies could neutralize both WT SARS-CoV-2 and BA.1 and are enriched on epitopes on spike that do not bind ACE2. However, most of these cross-reactive neutralizing antibodies are evaded by spike mutants L452Q, L452R and F486V. BA.1 infection can also induce new clones of BA.1-specific antibodies that potently neutralize BA.1. Nevertheless, these neutralizing antibodies are largely evaded by BA.2 and BA.4/BA.5 owing to D405N and F486V mutations, and react weakly to pre-Omicron variants, exhibiting narrow neutralization breadths. The therapeutic neutralizing antibodies bebtelovimab and cilgavimab can effectively neutralize BA.2.12.1 and BA.4/BA.5, whereas the S371F, D405N and R408S mutations undermine most broadly sarbecovirus-neutralizing antibodies. Together, our results indicate that Omicron may evolve mutations to evade the humoral immunity elicited by BA.1 infection, suggesting that BA.1-derived vaccine boosters may not achieve broad-spectrum protection against new Omicron variants.
External links	Nature / PubMed:35714668 / PubMed Central
Methods	EM (single particle)
Resolution	3.07 - 3.74 Å
Structure data	32718 7wr8 EMDB-32718, PDB-7wr8: Local CryoEM structure of the SARS-CoV-2 S6P(B.1.1.529) in complex with BD55-3152 Fab Method: EM (single particle) / Resolution: 3.5 Å 32732 7wrl EMDB-32732, PDB-7wrl: Local structure of BD55-1239 Fab and SARS-COV2 Omicron RBD complex Method: EM (single particle) / Resolution: 3.51 Å 32734 7wro EMDB-32734, PDB-7wro: Local structure of BD55-3372 and delta spike Method: EM (single particle) / Resolution: 3.4 Å 32738 7wrz EMDB-32738, PDB-7wrz: Local resolution of BD55-5840 Fab and SARS-COV2 Omicron RBD Method: EM (single particle) / Resolution: 3.26 Å 33019 7x6a EMDB-33019, PDB-7x6a: SARS-CoV-2 BA.2 variant spike protein in complex with Fab BD55-5840 Method: EM (single particle) / Resolution: 3.5 Å 33210 7xiw EMDB-33210, PDB-7xiw: SARS-CoV-2 Omicron BA.2 variant spike (state 1) Method: EM (single particle) / Resolution: 3.62 Å 33211 7xix EMDB-33211, PDB-7xix: SARS-CoV-2 Omicron BA.2 variant spike (state 2) Method: EM (single particle) / Resolution: 3.25 Å 33212 7xiy EMDB-33212, PDB-7xiy: SARS-CoV-2 Omicron BA.3 variant spike Method: EM (single particle) / Resolution: 3.07 Å 33213 7xiz EMDB-33213, PDB-7xiz: SARS-CoV-2 Omicron BA.3 variant spike (local) Method: EM (single particle) / Resolution: 3.74 Å 33323 7xnq EMDB-33323, PDB-7xnq: SARS-CoV-2 Omicron BA.4 variant spike Method: EM (single particle) / Resolution: 3.52 Å 33324 7xnr EMDB-33324, PDB-7xnr: SARS-CoV-2 Omicron BA.2.13 variant spike Method: EM (single particle) / Resolution: 3.49 Å 33325 7xns EMDB-33325, PDB-7xns: SARS-CoV-2 Omicron BA.2.12.1 variant spike Method: EM (single particle) / Resolution: 3.48 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose
Source	homo sapiens (human) severe acute respiratory syndrome coronavirus 2 sars coronavirus b012 severe acute respiratory syndrome coronavirus
Keywords	VIRAL PROTEIN / antibody / complex / S6P / SARS-COV2 Omicron / VIRAL PROTEIN/IMMUNE SYSTEM / sars-cov-2 / VIRAL PROTEIN-IMMUNE SYSTEM complex / SARS-COV2 Omicron RBD / Omicron / Spike-Fab complex / BA.2 / spike / BA.3 / BA.4 / BA.2.13 / BA.2.12.1