Evidence map›Paper›PMID 39059371›Full record

ArticleMolecular cell2024

SARS-CoV-2 Omicron XBB lineage spike structures, conformations, antigenicity, and receptor recognition.

Qianyi E Zhang, Jared Lindenberger, Ruth J Parsons, Bhishem Thakur, Rob Parks, Chan Soo Park, Xiao Huang, Salam Sammour, Katarzyna Janowska, Taylor N Spence and 10 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular cell, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.

0numbers the graph read from it
0cells of the map it votes in
21citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

21 citing papers in PubMed.

  1. Article
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  5. Article
  6. Review
  7. Article
  8. Article
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  10. Article
  11. Article
  12. Article
  13. Predicting high-fitness viral protein variants with Bayesian active learning and biophysics.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  14. Article
  15. Article
  16. Article
  17. Article
  18. Structural Immunology of SARS-CoV-2.Immunological reviews · 2025
    Review
  19. Article
  20. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

20 authors.

Qianyi E ZhangDuke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Biochemistry, Durham, NC 27710, USA.
Jared LindenbergerDuke University, Duke Human Vaccine Institute, Durham, NC 27710, USA.
Ruth J ParsonsDuke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Biochemistry, Durham, NC 27710, USA.
Bhishem ThakurDuke University, Duke Human Vaccine Institute, Durham, NC 27710, USA.
Rob ParksDuke University, Duke Human Vaccine Institute, Durham, NC 27710, USA.
Chan Soo ParkDuke University, Duke Human Vaccine Institute, Durham, NC 27710, USA.
Xiao HuangDuke University, Duke Human Vaccine Institute, Durham, NC 27710, USA.
Salam SammourDuke University, Duke Human Vaccine Institute, Durham, NC 27710, USA.
Katarzyna JanowskaDuke University, Duke Human Vaccine Institute, Durham, NC 27710, USA.
Taylor N SpenceDuke University, Duke Human Vaccine Institute, Durham, NC 27710, USA.
Robert J EdwardsDuke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Medicine, Durham, NC 27710, USA.
Mitchell MartinDuke University, Duke Human Vaccine Institute, Durham, NC 27710, USA.
Wilton B WilliamsDuke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Surgery, Durham, NC 27710, USA; Duke University, Department of Integrative Immunology, Durham, NC 27710, USA.
Sophie GobeilDuke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Université Laval, Institut de Biologie Intégrative et des Systèmes (IBIS), Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Centre de Recherche en Infectiologie de l'Université Laval, PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Québec, QC, Canada.
David C MontefioriDuke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Surgery, Durham, NC 27710, USA.
Bette KorberTheoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; The New Mexico Consortium, Los Alamos, NM 87544, USA.
Kevin O SaundersDuke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Surgery, Durham, NC 27710, USA; Duke University, Department of Integrative Immunology, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA.
Barton F HaynesDuke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Medicine, Durham, NC 27710, USA; Duke University, Department of Integrative Immunology, Durham, NC 27710, USA.
Rory HendersonDuke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Medicine, Durham, NC 27710, USA.
Priyamvada AcharyaDuke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Biochemistry, Durham, NC 27710, USA; Duke University, Department of Surgery, Durham, NC 27710, USA. Electronic address: priyamvada.acharya@duke.edu.

Funding

Project 4: Computational panbetaCoV immunogen designP01AI158571 · NIAID · DUKE UNIVERSITY · PI HAYNES, BARTON F. · 2021 to 2023
$28.0M
Effect of natural and engineered variations on structure and biophysics of SARS-CoV-2 spikeR01AI165947 · NIAID · DUKE UNIVERSITY · PI Priyamvada Acharya, Rory Henderson · 2022 to 2026
$3.8M
Structural characterization of Fab-dimerized glycan-reactive antibodies that neutralize HIV-1R01AI165147 · NIAID · DUKE UNIVERSITY · PI ACHARYA, PRIYAMVADA, WILLIAMS, WILTON B · 2021 to 2025
$3.4M
Data commons for 'omic, microscopy and analysis core facilitiesS10OD018164 · OD · DUKE UNIVERSITY · PI WRAY, GREGORY A. · 2014 to 2014
$598k
NIAID NIH HHS P01 AI158571NIAID NIH HHS R01 AI165147NIAID NIH HHS R01 AI165947NIH HHS S10 OD018164
6 · The paper itself

Abstract

A recombinant lineage of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant, named XBB, appeared in late 2022 and evolved descendants that successively swept local and global populations. XBB lineage members were noted for their improved immune evasion and transmissibility. Here, we determine cryoelectron microscopy (cryo-EM) structures of XBB.1.5, XBB.1.16, EG.5, and EG.5.1 spike (S) ectodomains to reveal reinforced 3-receptor binding domain (RBD)-down receptor-inaccessible closed states mediated by interprotomer RBD interactions previously observed in BA.1 and BA.2. Improved XBB.1.5 and XBB.1.16 RBD stability compensated for stability loss caused by early Omicron mutations, while the F456L substitution reduced EG.5 RBD stability. S1 subunit mutations had long-range impacts on conformation and epitope presentation in the S2 subunit. Our results reveal continued S protein evolution via simultaneous optimization of multiple parameters, including stability, receptor binding, and immune evasion, and the dramatic effects of relatively few residue substitutions in altering the S protein conformational landscape.

Indexed as

COVID-19Cryoelectron MicroscopyMutationProtein ConformationSARS-CoV-2Spike Glycoprotein, CoronavirusBinding SitesHumansImmune EvasionModels, MolecularProtein BindingProtein DomainsSpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2allosteryconformational changecryo-EMEG.5receptor binding domainthermostabilityvaccine boostervirus evolutionXBB.1.16XBB.1.5

Identifiers

PMID39059371
PMCPMC11366207

What Socratic holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.