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	Altered receptor binding, antibody evasion and retention of T cell recognition by the SARS-CoV-2 XBB.1.5 spike protein.
Journal, issue, pages	Nat Commun, Vol. 15, Issue 1, Page 1854, Year 2024
Publish date	Feb 29, 2024
Authors	Dhiraj Mannar / James W Saville / Chad Poloni / Xing Zhu / Alison Bezeruk / Keith Tidey / Sana Ahmed / Katharine S Tuttle / Faezeh Vahdatihassani / Spencer Cholak / Laura Cook / Theodore S Steiner / Sriram Subramaniam /
PubMed Abstract	The XBB.1.5 variant of SARS-CoV-2 has rapidly achieved global dominance and exhibits a high growth advantage over previous variants. Preliminary reports suggest that the success of XBB.1.5 stems from ...The XBB.1.5 variant of SARS-CoV-2 has rapidly achieved global dominance and exhibits a high growth advantage over previous variants. Preliminary reports suggest that the success of XBB.1.5 stems from mutations within its spike glycoprotein, causing immune evasion and enhanced receptor binding. We present receptor binding studies that demonstrate retention of binding contacts with the human ACE2 receptor and a striking decrease in binding to mouse ACE2 due to the revertant R493Q mutation. Despite extensive evasion of antibody binding, we highlight a region on the XBB.1.5 spike protein receptor binding domain (RBD) that is recognized by serum antibodies from a donor with hybrid immunity, collected prior to the emergence of the XBB.1.5 variant. T cell assays reveal high frequencies of XBB.1.5 spike-specific CD4 and CD8 T cells amongst donors with hybrid immunity, with the CD4 T cells skewed towards a Th1 cell phenotype and having attenuated effector cytokine secretion as compared to ancestral spike protein-specific cells. Thus, while the XBB.1.5 variant has retained efficient human receptor binding and gained antigenic alterations, it remains susceptible to recognition by T cells induced via vaccination and previous infection.
External links	Nat Commun / PubMed:38424106 / PubMed Central
Methods	EM (single particle)
Resolution	2.68 - 20.0 Å
Structure data	43320 8vkk EMDB-43320, PDB-8vkk: Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein Method: EM (single particle) / Resolution: 2.81 Å 43321 8vkl EMDB-43321, PDB-8vkl: Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with mouse ACE2 (conformation 2) Method: EM (single particle) / Resolution: 2.91 Å 43322 8vkm EMDB-43322, PDB-8vkm: Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with mouse ACE2 (conformation 1) Method: EM (single particle) / Resolution: 2.83 Å 43323 8vkn EMDB-43323, PDB-8vkn: Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with mouse ACE2 (focused refinement of RBD and mouse ACE2) Method: EM (single particle) / Resolution: 2.93 Å 43324 8vko EMDB-43324, PDB-8vko: Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with human ACE2 Method: EM (single particle) / Resolution: 2.68 Å 43325 8vkp EMDB-43325, PDB-8vkp: Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with human ACE2 (focused refinement of RBD and ACE2) Method: EM (single particle) / Resolution: 2.77 Å EMDB-43326: Negative Stain EM Reconstructions of SARS-CoV-2 spike proteins mixed with polyclonal antibodies from donor 4. Method: EM (single particle) / Resolution: 20.0 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose
Source	severe acute respiratory syndrome coronavirus 2 mus musculus (house mouse) homo sapiens (human)
Keywords	VIRAL PROTEIN/IMMUNE SYSTEM / Complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex