8DM0
Cryo-EM structure of SARS-CoV-2 D614G spike protein in complex with VH ab6 (focused refinement of NTD and VH ab6)
Summary for 8DM0
| Entry DOI | 10.2210/pdb8dm0/pdb |
| EMDB information | 27522 |
| Descriptor | Spike glycoprotein, VH ab6, 2-acetamido-2-deoxy-beta-D-glucopyranose (3 entities in total) |
| Functional Keywords | sars-cov-2, glycoprotein, fusion protein, viral protein, viral protein-immune system complex, vh ab6, viral protein/immune system |
| Biological source | Severe acute respiratory syndrome coronavirus 2 More |
| Total number of polymer chains | 2 |
| Total formula weight | 155702.30 |
| Authors | Zhu, X.,Mannar, D.,Saville, J.W.,Srivastava, S.S.,Berezuk, A.M.,Zhou, S.,Tuttle, K.S.,Subramaniam, S. (deposition date: 2022-07-08, release date: 2022-08-31, Last modification date: 2024-10-30) |
| Primary citation | Mannar, D.,Saville, J.W.,Sun, Z.,Zhu, X.,Marti, M.M.,Srivastava, S.S.,Berezuk, A.M.,Zhou, S.,Tuttle, K.S.,Sobolewski, M.D.,Kim, A.,Treat, B.R.,Da Silva Castanha, P.M.,Jacobs, J.L.,Barratt-Boyes, S.M.,Mellors, J.W.,Dimitrov, D.S.,Li, W.,Subramaniam, S. SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Nat Commun, 13:4696-4696, 2022 Cited by 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 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. PubMed: 35982054DOI: 10.1038/s41467-022-32262-8 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.21 Å) |
Structure validation
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