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	Conformational dynamics of the Beta and Kappa SARS-CoV-2 spike proteins and their complexes with ACE2 receptor revealed by cryo-EM.
Journal, issue, pages	Nat Commun, Vol. 12, Issue 1, Page 7345, Year 2021
Publish date	Dec 20, 2021
Authors	Yifan Wang / Cong Xu / Yanxing Wang / Qin Hong / Chao Zhang / Zuyang Li / Shiqi Xu / Qinyu Zuo / Caixuan Liu / Zhong Huang / Yao Cong /
PubMed Abstract	The emergence of SARS-CoV-2 Kappa and Beta variants with enhanced transmissibility and resistance to neutralizing antibodies has created new challenges for the control of the ongoing COVID-19 ...The emergence of SARS-CoV-2 Kappa and Beta variants with enhanced transmissibility and resistance to neutralizing antibodies has created new challenges for the control of the ongoing COVID-19 pandemic. Understanding the structural nature of Kappa and Beta spike (S) proteins and their association with ACE2 is of significant importance. Here we present two cryo-EM structures for each of the Kappa and Beta spikes in the open and open-prone transition states. Compared with wild-type (WT) or G614 spikes, the two variant spikes appear more untwisted/open especially for Beta, and display a considerable population shift towards the open state as well as more pronounced conformational dynamics. Moreover, we capture four conformational states of the S-trimer/ACE2 complex for each of the two variants, revealing an enlarged conformational landscape for the Kappa and Beta S-ACE2 complexes and pronounced population shift towards the three RBDs up conformation. These results implicate that the mutations in Kappa and Beta may modify the kinetics of receptor binding and viral fusion to improve virus fitness. Combined with biochemical analysis, our structural study shows that the two variants are enabled to efficiently interact with ACE2 receptor despite their sensitive ACE2 binding surface is modified to escape recognition by some potent neutralizing MAbs. Our findings shed new light on the pathogenicity and immune evasion mechanism of the Beta and Kappa variants.
External links	Nat Commun / PubMed:34930910 / PubMed Central
Methods	EM (single particle)
Resolution	3.2 - 4.0 Å
Structure data	32167 7vx1 EMDB-32167, PDB-7vx1: SARS-CoV-2 Beta variant spike protein in open state Method: EM (single particle) / Resolution: 3.5 Å 32168 7vx4 EMDB-32168, PDB-7vx4: ACE2-RBD in SARS-CoV-2 Beta variant S-ACE2 complex Method: EM (single particle) / Resolution: 3.9 Å 32169 7vx5 EMDB-32169, PDB-7vx5: ACE2-RBD in SARS-CoV-2 Kappa variant S-ACE2 complex Method: EM (single particle) / Resolution: 3.8 Å 32170 7wev EMDB-32170: SARS-CoV-2 Beta variant spike protein in transition state PDB-7wev: SARS-COV-2 BETA VARIANT SPIKE PROTEIN IN TRANSITION STATE Method: EM (single particle) / Resolution: 3.6 Å 32172 7vx9 EMDB-32172, PDB-7vx9: SARS-CoV-2 Kappa variant spike protein in complex wth ACE2, state C1 Method: EM (single particle) / Resolution: 4.0 Å 32173 7vxa EMDB-32173, PDB-7vxa: SARS-CoV-2 Kappa variant spike protein in complex with ACE2, state C2a Method: EM (single particle) / Resolution: 3.9 Å 32174 7vxb EMDB-32174, PDB-7vxb: SARS-CoV-2 Kappa variant spike protein in C2b state Method: EM (single particle) / Resolution: 3.9 Å 32175 7vxc EMDB-32175, PDB-7vxc: SARS-CoV-2 Kappa variant spike protein in C3 state Method: EM (single particle) / Resolution: 3.9 Å 32176 7vxd EMDB-32176, PDB-7vxd: SARS-CoV-2 spike protein in complex with ACE2, Beta variant, C1 state Method: EM (single particle) / Resolution: 4.0 Å 32177 7vxe EMDB-32177, PDB-7vxe: SARS-CoV-2 Kappa variant spike protein in open state Method: EM (single particle) / Resolution: 3.2 Å 32178 7vxf EMDB-32178, PDB-7vxf: SARS-CoV-2 spike protein in complex with ACE2, Beta variant, C2B state Method: EM (single particle) / Resolution: 3.6 Å 32180 7vxi EMDB-32180, PDB-7vxi: SARS-CoV-2 Kappa variant spike protein in transition state Method: EM (single particle) / Resolution: 3.4 Å 32182 7vxk EMDB-32182, PDB-7vxk: SARS-CoV-2 spike protein in complex with ACE2, Beta variant, C2A state Method: EM (single particle) / Resolution: 3.7 Å 32184 7vxm EMDB-32184, PDB-7vxm: SARS-CoV-2 spike protein in complex with ACE2, Beta variant, C3 state Method: EM (single particle) / Resolution: 3.6 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine
Source	severe acute respiratory syndrome coronavirus 2 homo sapiens (human) omo sapiens (human)
Keywords	VIRAL PROTEIN / SARS-CoV-2 / coronavirus / Beta variant / B.1.351 lineage / spike protein / Angiotensin-converting enzyme 2 / Kappa variant / B.1.617.1 lineage / VIRAL PROTEIN/HYDROLASE / VIRAL PROTEIN-HYDROLASE complex / SPIK PROTEIN