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	Effect of SARS-CoV-2 B.1.1.7 mutations on spike protein structure and function.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 28, Issue 9, Page 731-739, Year 2021
Publish date	Aug 12, 2021
Authors	Tzu-Jing Yang / Pei-Yu Yu / Yuan-Chih Chang / Kang-Hao Liang / Hsian-Cheng Tso / Meng-Ru Ho / Wan-Yu Chen / Hsiu-Ting Lin / Han-Chung Wu / Shang-Te Danny Hsu /
PubMed Abstract	The B.1.1.7 variant of SARS-CoV-2 first detected in the UK harbors amino-acid substitutions and deletions in the spike protein that potentially enhance host angiotensin conversion enzyme 2 (ACE2) ...The B.1.1.7 variant of SARS-CoV-2 first detected in the UK harbors amino-acid substitutions and deletions in the spike protein that potentially enhance host angiotensin conversion enzyme 2 (ACE2) receptor binding and viral immune evasion. Here we report cryo-EM structures of the spike protein of B.1.1.7 in the apo and ACE2-bound forms. The apo form showed one or two receptor-binding domains (RBDs) in the open conformation, without populating the fully closed state. All three RBDs were engaged in ACE2 binding. The B.1.1.7-specific A570D mutation introduces a molecular switch that could modulate the opening and closing of the RBD. The N501Y mutation introduces a π-π interaction that enhances RBD binding to ACE2 and abolishes binding of a potent neutralizing antibody (nAb). Cryo-EM also revealed how a cocktail of two nAbs simultaneously bind to all three RBDs, and demonstrated the potency of the nAb cocktail to neutralize different SARS-CoV-2 pseudovirus strains, including B.1.1.7.
External links	Nat Struct Mol Biol / PubMed:34385690
Methods	EM (single particle)
Resolution	3.2 - 4.03 Å
Structure data	31069 7edf EMDB-31069, PDB-7edf: Cryo-EM structure of SARS-CoV-2 S-UK variant (B.1.1.7), one RBD-up conformation 1 Method: EM (single particle) / Resolution: 3.2 Å 31070 7edg EMDB-31070, PDB-7edg: Cryo-EM structure of SARS-CoV-2 S-UK variant (B.1.1.7), one RBD-up conformation 2 Method: EM (single particle) / Resolution: 3.2 Å 31071 7edh EMDB-31071, PDB-7edh: Cryo-EM structure of SARS-CoV-2 S-UK variant (B.1.1.7), one RBD-up conformation 3 Method: EM (single particle) / Resolution: 3.6 Å 31072 7edi EMDB-31072, PDB-7edi: Cryo-EM structure of SARS-CoV-2 S-UK variant (B.1.1.7), two RBD-up conformation Method: EM (single particle) / Resolution: 3.3 Å 31073 7edj EMDB-31073, PDB-7edj: Cryo-EM structure of SARS-CoV-2 S-UK variant (B.1.1.7) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain Method: EM (single particle) / Resolution: 3.3 Å 31074 7eh5 EMDB-31074: Cryo-EM structure of SARS-CoV-2 S-D614G variant in complex with neutralizing antibodies, RBD-chAb-15 and RBD-chAb45 PDB-7eh5: Cryo-EM structure of SARS-CoV-2 S-D614G variant in complex with neutralizing antibodies, RBD-chAb15 and RBD-chAb45 Method: EM (single particle) / Resolution: 4.03 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine
Source	severe acute respiratory syndrome coronavirus 2 homo sapiens (human)
Keywords	VIRAL PROTEIN / SARS-CoV-2 / Spike protein / Neutralizing antibody