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	Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies.
Journal, issue, pages	PLoS Biol, Vol. 19, Issue 4, Page e3001237, Year 2021
Publish date	Apr 29, 2021
Authors	Xing Zhu / Dhiraj Mannar / Shanti S Srivastava / Alison M Berezuk / Jean-Philippe Demers / James W Saville / Karoline Leopold / Wei Li / Dimiter S Dimitrov / Katharine S Tuttle / Steven Zhou / Sagar Chittori / Sriram Subramaniam /
PubMed Abstract	The recently reported "UK variant" (B.1.1.7) of SARS-CoV-2 is thought to be more infectious than previously circulating strains as a result of several changes, including the N501Y mutation. We ...The recently reported "UK variant" (B.1.1.7) of SARS-CoV-2 is thought to be more infectious than previously circulating strains as a result of several changes, including the N501Y mutation. We present a 2.9-Å resolution cryo-electron microscopy (cryo-EM) structure of the complex between the ACE2 receptor and N501Y spike protein ectodomains that shows Y501 inserted into a cavity at the binding interface near Y41 of ACE2. This additional interaction provides a structural explanation for the increased ACE2 affinity of the N501Y mutant, and likely contributes to its increased infectivity. However, this mutation does not result in large structural changes, enabling important neutralization epitopes to be retained in the spike receptor binding domain. We confirmed this through biophysical assays and by determining cryo-EM structures of spike protein ectodomains bound to 2 representative potent neutralizing antibody fragments.
External links	PLoS Biol / PubMed:33914735 / PubMed Central
Methods	EM (single particle)
Resolution	2.66 - 3.32 Å
Structure data	23872 7mjg EMDB-23872, PDB-7mjg: Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain Method: EM (single particle) / Resolution: 2.81 Å 23873 7mjh EMDB-23873, PDB-7mjh: Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to VH ab8 Method: EM (single particle) / Resolution: 2.66 Å 23874 7mji EMDB-23874, PDB-7mji: Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to VH ab8 (focused refinement of RBD and VH ab8) Method: EM (single particle) / Resolution: 2.81 Å 23875 7mjj EMDB-23875, PDB-7mjj: Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to Fab ab1 (class 1) Method: EM (single particle) / Resolution: 3.32 Å 23876 7mjk EMDB-23876, PDB-7mjk: Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to Fab ab1 (class 2) Method: EM (single particle) / Resolution: 2.73 Å 23877 7mjl EMDB-23877, PDB-7mjl: Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to Fab ab1 (focused refinement of RBD and Fab ab1) Method: EM (single particle) / Resolution: 2.95 Å 23878 7mjm EMDB-23878, PDB-7mjm: Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to human ACE2 ectodomain Method: EM (single particle) / Resolution: 2.83 Å 23879 7mjn EMDB-23879, PDB-7mjn: Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to human ACE2 ectodomain (focused refinement of RBD and ACE2) Method: EM (single particle) / Resolution: 3.29 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine
Source	severe acute respiratory syndrome coronavirus 2 synthetic construct (others) homo sapiens (human)
Keywords	VIRAL PROTEIN / SARS-CoV-2 / glycoprotein / fusion protein / VH ab8 / neutralizing antibody / Viral Protein/Immune System / Viral Protein-Immune System complex / Fab ab1 / ACE2 / VIRAL PROTEIN/Hydrolase / VIRAL PROTEIN-Hydrolase complex