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- PDB-8vye: SARS-CoV-2 S (C.37 Lambda variant) plus S309, S2L20, and S2X303 Fabs -
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Open data
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Basic information
Entry | Database: PDB / ID: 8vye | ||||||
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Title | SARS-CoV-2 S (C.37 Lambda variant) plus S309, S2L20, and S2X303 Fabs | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / sars-cov-2 / coronavirus / lambda / s309 / 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 | ||||||
Function / homology | ![]() Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||
![]() | McCallum, M. / Veesler, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Quantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence features. Authors: Craig A Magaret / Li Li / Allan C deCamp / Morgane Rolland / Michal Juraska / Brian D Williamson / James Ludwig / Cindy Molitor / David Benkeser / Alex Luedtke / Brian Simpkins / Fei Heng / ...Authors: Craig A Magaret / Li Li / Allan C deCamp / Morgane Rolland / Michal Juraska / Brian D Williamson / James Ludwig / Cindy Molitor / David Benkeser / Alex Luedtke / Brian Simpkins / Fei Heng / Yanqing Sun / Lindsay N Carpp / Hongjun Bai / Bethany L Dearlove / Elena E Giorgi / Mandy Jongeneelen / Boerries Brandenburg / Matthew McCallum / John E Bowen / David Veesler / Jerald Sadoff / Glenda E Gray / Sanne Roels / An Vandebosch / Daniel J Stieh / Mathieu Le Gars / Johan Vingerhoets / Beatriz Grinsztejn / Paul A Goepfert / Leonardo Paiva de Sousa / Mayara Secco Torres Silva / Martin Casapia / Marcelo H Losso / Susan J Little / Aditya Gaur / Linda-Gail Bekker / Nigel Garrett / Carla Truyers / Ilse Van Dromme / Edith Swann / Mary A Marovich / Dean Follmann / Kathleen M Neuzil / Lawrence Corey / Alexander L Greninger / Pavitra Roychoudhury / Ollivier Hyrien / Peter B Gilbert / ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 ...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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 856.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 122.9 KB | Display | |
Data in CIF | ![]() | 198.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 43658MC ![]() 8vyfC ![]() 8vygC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Antibody , 6 types, 18 molecules BFPCGQAIRDJSHMTLNU
#2: Antibody | Mass: 13541.036 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Antibody | Mass: 11829.141 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Antibody | Mass: 14005.526 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #5: Antibody | Mass: 11315.497 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #6: Antibody | Mass: 13737.725 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #7: Antibody | Mass: 11270.294 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Protein / Sugars , 2 types, 60 molecules KEO![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 140929.156 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Lambda spike glycoprotein Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() #8: Sugar | ChemComp-NAG / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: SARS-CoV-2 S C.37 (Lambda variant) plus S309, S2L20, and S2X303 Fabs Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 30000 nm / Nominal defocus min: 2000 nm |
Image recording | Electron dose: 63 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 147418 / Symmetry type: POINT |