8VYF

SARS-CoV-2 S NTD (C.37 Lambda variant) plus S2L20 and S2X303 Fabs, local refinement

This is a non-PDB format compatible entry.

Summary for 8VYF

• Entry DOI: 10.2210/pdb8vyf/pdb
• Related: 8VYE 8VYG
• EMDB information: 43659
• Descriptor: Spike glycoprotein, S2L20 Heavy Chain, S2L20 Light Chain, ... (8 entities in total)
• Functional Keywords: sars-cov-2, coronavirus, lambda, s2l20, s2x303, c.37, antibody, fab, s protein, spike, fusion protein, structural genomics, seattle structural genomics center for infectious disease, ssgcid, viral protein, viral protein-immune system complex, viral protein/immune system
• Biological source: Severe acute respiratory syndrome coronavirus 2; More
• Total number of polymer chains: 5
• Total formula weight: 193848.74

Authors

McCallum, M.,Veesler, D.,Seattle Structural Genomics Center for Infectious Disease (SSGCID) (deposition date: 2024-02-08, release date: 2024-03-27, Last modification date: 2024-11-06)

Primary citation

Magaret, C.A.,Li, L.,deCamp, A.C.,Rolland, M.,Juraska, M.,Williamson, B.D.,Ludwig, J.,Molitor, C.,Benkeser, D.,Luedtke, A.,Simpkins, B.,Heng, F.,Sun, Y.,Carpp, L.N.,Bai, H.,Dearlove, B.L.,Giorgi, E.E.,Jongeneelen, M.,Brandenburg, B.,McCallum, M.,Bowen, J.E.,Veesler, D.,Sadoff, J.,Gray, G.E.,Roels, S.,Vandebosch, A.,Stieh, D.J.,Le Gars, M.,Vingerhoets, J.,Grinsztejn, B.,Goepfert, P.A.,de Sousa, L.P.,Silva, M.S.T.,Casapia, M.,Losso, M.H.,Little, S.J.,Gaur, A.,Bekker, L.G.,Garrett, N.,Truyers, C.,Van Dromme, I.,Swann, E.,Marovich, M.A.,Follmann, D.,Neuzil, K.M.,Corey, L.,Greninger, A.L.,Roychoudhury, P.,Hyrien, O.,Gilbert, P.B.
Quantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence features.
Nat Commun, 15:2175-2175, 2024

PubMed Abstract: In the ENSEMBLE randomized, placebo-controlled phase 3 trial (NCT04505722), estimated single-dose Ad26.COV2.S vaccine efficacy (VE) was 56% against moderate to severe-critical COVID-19. SARS-CoV-2 Spike sequences were determined from 484 vaccine and 1,067 placebo recipients who acquired COVID-19. In this set of prespecified analyses, we show that in Latin America, VE was significantly lower against Lambda vs. Reference and against Lambda vs. non-Lambda [family-wise error rate (FWER) p < 0.05]. VE differed by residue match vs. mismatch to the vaccine-insert at 16 amino acid positions (4 FWER p < 0.05; 12 q-value ≤ 0.20); significantly decreased with physicochemical-weighted Hamming distance to the vaccine-strain sequence for Spike, receptor-binding domain, N-terminal domain, and S1 (FWER p < 0.001); differed (FWER ≤ 0.05) by distance to the vaccine strain measured by 9 antibody-epitope escape scores and 4 NTD neutralization-impacting features; and decreased (p = 0.011) with neutralization resistance level to vaccinee sera. VE against severe-critical COVID-19 was stable across most sequence features but lower against the most distant viruses.

PubMed: 38467646
DOI: 10.1038/s41467-024-46536-w

Experimental method

ELECTRON MICROSCOPY (3.2 Å)