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	SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Journal, issue, pages	Nat Commun, Vol. 13, Issue 1, Page 4696, Year 2022
Publish date	Aug 18, 2022
Authors	Dhiraj Mannar / James W Saville / Zehua Sun / Xing Zhu / Michelle M Marti / Shanti S Srivastava / Alison M Berezuk / Steven Zhou / Katharine S Tuttle / Michele D Sobolewski / Andrew Kim / Benjamin R Treat / Priscila Mayrelle Da Silva Castanha / Jana L Jacobs / Simon M Barratt-Boyes / John W Mellors / Dimiter S Dimitrov / Wei Li / Sriram Subramaniam /
PubMed Abstract	Mutations in the spike glycoproteins of SARS-CoV-2 variants of concern have independently been shown to enhance aspects of spike protein fitness. Here, we describe an antibody fragment (V ab6) that ...Mutations in the spike glycoproteins of SARS-CoV-2 variants of concern have independently been shown to enhance aspects of spike protein fitness. Here, we describe an antibody fragment (V ab6) that neutralizes all major variants including the recently emerged BA.1 and BA.2 Omicron subvariants, with a unique mode of binding revealed by cryo-EM studies. Further, we provide a comparative analysis of the mutational effects within previously emerged variant spikes and identify the structural role of mutations within the NTD and RBD in evading antibody neutralization. Our analysis shows that the highly mutated Gamma N-terminal domain exhibits considerable structural rearrangements, partially explaining its decreased neutralization by convalescent sera. Our results provide mechanistic insights into the structural, functional, and antigenic consequences of SARS-CoV-2 spike mutations and highlight a spike protein vulnerability that may be exploited to achieve broad protection against circulating variants.
External links	Nat Commun / PubMed:35982054 / PubMed Central
Methods	EM (single particle)
Resolution	2.16 - 3.21 Å
Structure data	27502 8dli EMDB-27502, PDB-8dli: Cryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike protein Method: EM (single particle) / Resolution: 2.56 Å 27503 8dlj EMDB-27503, PDB-8dlj: Cryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike protein in complex with human ACE2 Method: EM (single particle) / Resolution: 2.91 Å 27504 8dlk EMDB-27504, PDB-8dlk: Cryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike protein in complex with human ACE2 (focused refinement of RBD and ACE2) Method: EM (single particle) / Resolution: 3.04 Å 27505 8dll EMDB-27505, PDB-8dll: Cryo-EM structure of SARS-CoV-2 Beta (B.1.351) spike protein Method: EM (single particle) / Resolution: 2.56 Å 27506 8dlm EMDB-27506, PDB-8dlm: Cryo-EM structure of SARS-CoV-2 Beta (B.1.351) spike protein in complex with human ACE2 Method: EM (single particle) / Resolution: 2.89 Å 27507 8dln EMDB-27507, PDB-8dln: Cryo-EM structure of SARS-CoV-2 Beta (B.1.351) spike protein in complex with human ACE2 (focused refinement of RBD and ACE2) Method: EM (single particle) / Resolution: 3.04 Å 27508 8dlo EMDB-27508, PDB-8dlo: Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein Method: EM (single particle) / Resolution: 2.25 Å 27509 8dlp EMDB-27509, PDB-8dlp: Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with human ACE2 Method: EM (single particle) / Resolution: 2.64 Å 27510 8dlq EMDB-27510, PDB-8dlq: Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with human ACE2 (focused refinement of RBD and ACE2) Method: EM (single particle) / Resolution: 2.77 Å EMDB-27511: Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4-8 Method: EM (single particle) / Resolution: 2.59 Å 27512 8dlr EMDB-27512, PDB-8dlr: Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4-8 (focused refinement of NTD and 4-8) Method: EM (single particle) / Resolution: 2.51 Å EMDB-27513: Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4A8 Method: EM (single particle) / Resolution: 2.59 Å 27514 8dls EMDB-27514, PDB-8dls: Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4A8 (focused refinement of NTD and 4A8) Method: EM (single particle) / Resolution: 2.66 Å 27515 8dlt EMDB-27515, PDB-8dlt: Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein Method: EM (single particle) / Resolution: 2.4 Å 27516 8dlu EMDB-27516, PDB-8dlu: Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with human ACE2 Method: EM (single particle) / Resolution: 3.14 Å 27517 8dlv EMDB-27517, PDB-8dlv: Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with human ACE2 (focused refinement of RBD and ACE2) Method: EM (single particle) / Resolution: 3.11 Å 27518 8dlw EMDB-27518, PDB-8dlw: Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with Fab S2M11 Method: EM (single particle) / Resolution: 2.16 Å 27519 8dlx EMDB-27519, PDB-8dlx: Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with VH ab6 Method: EM (single particle) / Resolution: 2.45 Å 27520 8dly EMDB-27520, PDB-8dly: Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with VH ab6 (focused refinement of NTD and VH ab6) Method: EM (single particle) / Resolution: 3.0 Å 27521 8dlz EMDB-27521, PDB-8dlz: Cryo-EM structure of SARS-CoV-2 D614G spike protein in complex with VH ab6 Method: EM (single particle) / Resolution: 2.57 Å 27522 8dm0 EMDB-27522, PDB-8dm0: Cryo-EM structure of SARS-CoV-2 D614G spike protein in complex with VH ab6 (focused refinement of NTD and VH ab6) Method: EM (single particle) / Resolution: 3.21 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose
Source	severe acute respiratory syndrome coronavirus 2 homo sapiens (human)
Keywords	VIRAL PROTEIN / SARS-CoV-2 / glycoprotein / fusion protein / Viral Protein-Immune System complex / Alpha / B.1.1.7 / Viral Protein/Hydrolase / ACE2 / Viral Protein-Hydrolase complex / Beta / B.1.351 / Gamma / P.1 / 4-8 / 4A8 / Epsilon / B.1.429 / S2M11 / VH ab6 / VIRAL PROTEIN/IMMUNE SYSTEM