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	Molecular basis of receptor binding and antibody neutralization of Omicron.
Journal, issue, pages	Nature, Vol. 604, Issue 7906, Page 546-552, Year 2022
Publish date	Feb 28, 2022
Authors	Qin Hong / Wenyu Han / Jiawei Li / Shiqi Xu / Yifan Wang / Cong Xu / Zuyang Li / Yanxing Wang / Chao Zhang / Zhong Huang / Yao Cong /
PubMed Abstract	The SARS-CoV-2 Omicron variant exhibits striking immune evasion and is spreading rapidly worldwide. Understanding the structural basis of the high transmissibility and enhanced immune evasion of ...The SARS-CoV-2 Omicron variant exhibits striking immune evasion and is spreading rapidly worldwide. Understanding the structural basis of the high transmissibility and enhanced immune evasion of Omicron is of high importance. Here, using cryo-electron microscopy, we present both the closed and the open states of the Omicron spike (S) protein, which appear more compact than the counterparts of the G614 strain, potentially related to enhanced inter-protomer and S1-S2 interactions induced by Omicron residue substitution. The closed state showing dominant population may indicate a conformational masking mechanism for the immune evasion of Omicron. Moreover, we captured three states for the Omicron S-ACE2 complex, revealing that the substitutions on the Omicron RBM result in new salt bridges and hydrogen bonds, more favourable electrostatic surface properties, and an overall strengthened S-ACE2 interaction, in line with the observed higher ACE2 affinity of Omicron S than of G614. Furthermore, we determined the structures of Omicron S in complex with the Fab of S3H3, an antibody that is able to cross-neutralize major variants of concern including Omicron, elucidating the structural basis for S3H3-mediated broad-spectrum neutralization. Our findings shed light on the receptor engagement and antibody neutralization or evasion of Omicron and may also inform the design of broadly effective vaccines against SARS-CoV-2.
External links	Nature / PubMed:35228716
Methods	EM (single particle)
Resolution	3.1 - 4.04 Å
Structure data	32556 7wk2 EMDB-32556, PDB-7wk2: SARS-CoV-2 Omicron S-close Method: EM (single particle) / Resolution: 3.1 Å 32557 7wk3 EMDB-32557, PDB-7wk3: SARS-CoV-2 Omicron S-open Method: EM (single particle) / Resolution: 3.4 Å 32558 7wk4 EMDB-32558, PDB-7wk4: Cryo-EM structure of SARS-CoV-2 Omicron spike protein with ACE2, C1 state Method: EM (single particle) / Resolution: 3.69 Å 32559 7wk5 EMDB-32559, PDB-7wk5: Cryo-EM structure of Omicron S-ACE2, C2 state Method: EM (single particle) / Resolution: 3.66 Å 32560 7wk6 EMDB-32560, PDB-7wk6: Cryo-EM structure of SARS-CoV-2 Omicron spike protein with human ACE2 (focus refinement on RBD-1/ACE2) Method: EM (single particle) / Resolution: 3.67 Å 32562 7wk8 EMDB-32562, PDB-7wk8: SARS-CoV-2 Omicron spike protein SD1 in complex with S3H3 Fab Method: EM (single particle) / Resolution: 3.61 Å 32563 7wk9 EMDB-32563, PDB-7wk9: SARS-CoV-2 Omicron open state spike protein in complex with S3H3 Fab Method: EM (single particle) / Resolution: 3.48 Å 32564 7wka EMDB-32564, PDB-7wka: SARS-CoV-2 Omicron closed state spike protein in complex with S3H3 Fab Method: EM (single particle) / Resolution: 3.64 Å 32854 7wvn EMDB-32854, PDB-7wvn: SARS-CoV-2 Omicron S-open Method: EM (single particle) / Resolution: 3.4 Å 32855 7wvo EMDB-32855, PDB-7wvo: SARS-CoV-2 Omicron S-open-2 Method: EM (single particle) / Resolution: 3.41 Å 32856 7wvp EMDB-32856, PDB-7wvp: Cryo-EM structure of SARS-CoV-2 Omicron Spike protein with human ACE2 receptor, C2 state Method: EM (single particle) / Resolution: 3.7 Å 32857 7wvq EMDB-32857, PDB-7wvq: Cryo-EM structure of SARS-CoV-2 Omicron Spike protein with human ACE2 receptor, C3 state Method: EM (single particle) / Resolution: 4.04 Å
Source	severe acute respiratory syndrome coronavirus 2 mus musculus (house mouse) homo sapiens (human) severe acute respiratory syndrome coronavirus
Keywords	VIRAL PROTEIN / SARS-CoV-2 / coronavirus / Omicron variant / S-close / spike protein / S-open / HYDROLASE/VIRAL PROTEIN / Omicron / ACE2 / HYDROLASE-VIRAL PROTEIN complex / VIRAL PROTEIN/HYDROLASE / VIRAL PROTEIN-HYDROLASE complex / B.1.1.529 lineage / S-open-2