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	A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity.
Journal, issue, pages	Cell Rep Med, Vol. 5, Issue 5, Page 101553, Year 2024
Publish date	May 21, 2024
Authors	Chang Liu / Daming Zhou / Aiste Dijokaite-Guraliuc / Piyada Supasa / Helen M E Duyvesteyn / Helen M Ginn / Muneeswaran Selvaraj / Alexander J Mentzer / Raksha Das / Thushan I de Silva / Thomas G Ritter / Megan Plowright / Thomas A H Newman / Lizzie Stafford / Barbara Kronsteiner / Nigel Temperton / Yuan Lui / Martin Fellermeyer / Philip Goulder / Paul Klenerman / Susanna J Dunachie / Michael I Barton / Mikhail A Kutuzov / Omer Dushek / / Elizabeth E Fry / Juthathip Mongkolsapaya / Jingshan Ren / David I Stuart / Gavin R Screaton /
PubMed Abstract	BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible ...BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible for many infections in 2023. The global spread and plethora of mutations in BA.2.86 has caused concern that it may possess greater immune-evasive potential, leading to a new wave of infection. Here, we examine the ability of BA.2.86 to evade the antibody response to infection using a panel of vaccinated or naturally infected sera and find that it shows marginally less immune evasion than XBB.1.5. We locate BA.2.86 in the antigenic landscape of recent variants and look at its ability to escape panels of potent monoclonal antibodies generated against contemporary SARS-CoV-2 infections. We demonstrate, and provide a structural explanation for, increased affinity of BA.2.86 to ACE2, which may increase transmissibility.
External links	Cell Rep Med / PubMed:38723626 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.3 - 4.03 Å
Structure data	18639 8qsq EMDB-18639, PDB-8qsq: Locally refined SARS-CoV-2 BA-2.86 Spike receptor binding domain (RBD) complexed with angiotensin converting enzyme 2 (ACE2) Method: EM (single particle) / Resolution: 3.7 Å 18649 8qtd EMDB-18649, PDB-8qtd: Local refinement of SARS-CoV-2 BA.2.86 Spike and XBB-7 Fab Method: EM (single particle) / Resolution: 3.6 Å 19002 8r8k EMDB-19002, PDB-8r8k: XBB-4 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein Method: EM (single particle) / Resolution: 3.41 Å PDB-8qrf: SARS-CoV-2 delta RBD complexed with XBB-6 and beta-49 Fabs Method: X-RAY DIFFRACTION / Resolution: 3.7 Å PDB-8qrg: SARS-CoV-2 delta RBD complexed with XBB-2 Fab and NbC1 Method: X-RAY DIFFRACTION / Resolution: 2.3 Å PDB-8r80: SARS-CoV-2 Delta RBD in complex with XBB-9 Fab and an anti-Fab nanobody Method: X-RAY DIFFRACTION / Resolution: 4.03 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose ChemComp-GOL: GLYCEROL ChemComp-HOH: WATER
Source	homo sapiens (human) severe acute respiratory syndrome coronavirus 2 tequatrovirus t4 lama glama (llama) synthetic construct (others)
Keywords	VIRAL PROTEIN / Viral protein/immune system / SARS-CoV-2 / RBD / XBB-6 / Beta-49 / BA.2.86 / XBB.1.5 / immune system / ACE2 / Spike / glycoprotein / angiotensin converting enzyme 2 / receptor / coronavirus-2 / XBB-7 / XBB.1.5.10 / XBB.1.5.70 / Coronavirus / antibody / Fab / therapeutic / complex / neutralising / receptor binding domain / convalescent sera / XBB-4 / BA.2.12.1 / omicron variant / virus