EMD-38495

Single-particle
2.79 Å
EMD-38495 Deposition: 28/12/2023
Map released: 03/07/2024
Last modified: 23/10/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-38495

SARS-CoV-2 Omicron EG.5.1 RBD in complex with human ACE2 (local refined from the spike protein)

EMD-38495

Single-particle
2.79 Å
EMD-38495 Deposition: 28/12/2023
Map released: 03/07/2024
Last modified: 23/10/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Sample: SARS-CoV-2 Omicron EG.5.1 RBD (receptor binding domain) in complex with human ACE2 (angiotensin converting enzyme 2)
Fitted models: 8xn2 (Avg. Q-score: 0.355)

Deposition Authors: Li LJ, Gu YH, Shi KY, Qi JX, Gao GF
Spike structures, receptor binding, and immune escape of recently circulating SARS-CoV-2 Omicron BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 sub-variants.
Li L, Shi K, Gu Y, Xu Z, Shu C, Li D, Sun J , Cong M, Li X, Zhao X, Yu G , Hu S, Tan H, Qi J, Ma X, Liu K, Gao GF
(2024) Structure , 32 , 1055 - 1067.e6
PUBMED: 39013463
DOI: doi:10.1016/j.str.2024.06.012
ISSN: 0969-2126
ASTM: STRUE6
Abstract:
The recently emerged BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 variants have a growth advantage. In this study, we explore the structural bases of receptor binding and immune evasion for the Omicron BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 sub-variants. Our findings reveal that BA.2.86 exhibits strong receptor binding, whereas its JN.1 sub-lineage displays a decreased binding affinity to human ACE2 (hACE2). Through complex structure analyses, we observed that the reversion of R493Q in BA.2.86 receptor binding domain (RBD) plays a facilitating role in receptor binding, while the L455S substitution in JN.1 RBD restores optimal affinity. Furthermore, the structure of monoclonal antibody (mAb) S309 complexed with BA.2.86 RBD highlights the importance of the K356T mutation, which brings a new N-glycosylation motif, altering the binding pattern of mAbs belonging to RBD-5 represented by S309. These findings emphasize the importance of closely monitoring BA.2.86 and its sub-lineages to prevent another wave of SARS-CoV-2 infections.