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	Engineering a multivalent antibody nanoparticle to overcome SARS-CoV-2 Omicron immune evasion.
Journal, issue, pages	PLoS Pathog, Vol. 21, Issue 12, Page e1013744, Year 2025
Publish date	Dec 8, 2025
Authors	Hui Sun / Yanan Jiang / Miaolin Lan / Ming Zhou / Gangshun Yi / Juan Shen / Tingting Deng / Liqin Liu / Yang Huang / Yu Li / Jinfu Su / Yanling Lin / Zhenqin Chen / Lizhi Zhou / Tingting Li / Hai Yu / Tong Cheng / Yali Zhang / Lunzhi Yuan / Shaowei Li / Ying Gu / Peijun Zhang / Ningshao Xia / Qingbing Zheng /
PubMed Abstract	The rapid evolution of SARS-CoV-2 and the subsequent emergence of Omicron subvariants pose significant challenges to the efficacy of existing vaccines and therapeutics, including those previously ...The rapid evolution of SARS-CoV-2 and the subsequent emergence of Omicron subvariants pose significant challenges to the efficacy of existing vaccines and therapeutics, including those previously reported most broad neutralizing antibodies (bnAbs). Here, we investigated the molecular basis of the altered neutralization profile of a bnAb, 1C4, against recent variants. 1C4 is effective against early variants from Alpha to Omicron BQ.1, but is circumvented by BQ.1.1, XBB and thereafter variants, primarily due to an additional R346T mutation that diminishes its binding affinity. Cryo-electron microscopy analysis revealed that despite the loss of neutralizing potency, 1C4 retained residual binding to the spike protein of immune-evasive variants such as XBB, which harbor altered receptor-binding domain (RBD). Furthermore, 1C4 exhibited a diminished capacity to inhibit ACE2 engagement with Omicron variants, amplifying the intricacies of viral immune evasion tactics. To address this, we employed the mi3-SpyCatcher-based nanoparticle to polymerize 1C4 (mi3-1C4), which reestablished the neutralization potency against recent variants by enhancing avidity via multivalent binding. Such multivalent binding can promote efficient spike aggregation as well as viral cross-linking, thereby providing enhanced protection against both the infection of Beta and XBB variants in a hamster model. Together, our findings delineate the molecular landscape of immune evasion by neutralizing antibodies and provide strategic insight for the adaptation of antibody engineering to keep pace with viral evolution.
External links	PLoS Pathog / PubMed:41359663 / PubMed Central
Methods	EM (single particle)
Resolution	2.33 - 10.08 Å
Structure data	EMDB-60852: Cryo-EM structure of SARS-CoV-2 BA.5 spike protein in complex with nAb 1C4 (state 1) Method: EM (single particle) / Resolution: 3.45 Å EMDB-60862: Cryo-EM structure of SARS-CoV-2 BA.5 spike protein in complex with nAb 1C4 (state 2) Method: EM (single particle) / Resolution: 3.68 Å EMDB-60863: Cryo-EM structure of SARS-CoV-2 WT spike protein in complex with three-nAb 8H12, 3E2 and 1C4 Method: EM (single particle) / Resolution: 3.76 Å EMDB-60864: Cryo-EM structure of SARS-CoV-2 BA.1 spike protein in complex with three-nAb 8H12, 3E2 and 1C4 Method: EM (single particle) / Resolution: 3.95 Å EMDB-60963: Cryo-EM structure of SARS-CoV-2 XBB spike protein in complex with three-nAb 8H12, 3E2 and 1C4 Method: EM (single particle) / Resolution: 10.08 Å EMDB-60974: Cryo-EM structure of SARS-CoV-2 BA.2 spike protein in complex with three-nAb 8H12, 3E2 and 1C4 Method: EM (single particle) / Resolution: 3.82 Å EMDB-60975: Cryo-EM structure of SARS-CoV-2 BA.2.75 spike protein in complex with three-nAb 8H12, 3E2 and 1C4 Method: EM (single particle) / Resolution: 6.31 Å EMDB-60976: Cryo-EM structure of SARS-CoV-2 BA.5 spike protein in complex with three-nAb 8H12, 3E2 and 1C4 (state 1) Method: EM (single particle) / Resolution: 4.35 Å EMDB-60979: Cryo-EM structure of SARS-CoV-2 BA.5 spike protein in complex with three-nAb 8H12, 3E2 and 1C4 (state 2) Method: EM (single particle) / Resolution: 3.9 Å 62596 9kvj EMDB-62596, PDB-9kvj: Cryo-EM structure of SARS-CoV-2 BA.5 spike protein in complex with nAb 1C4 (local refinement) Method: EM (single particle) / Resolution: 3.82 Å 62597 9kvk EMDB-62597, PDB-9kvk: Cryo-EM structure of SARS-CoV-2 spike protein in complex with three-nAb 8H12, 3E2 and 1C4 Method: EM (single particle) / Resolution: 3.44 Å 62599 9kvq EMDB-62599, PDB-9kvq: Cryo-EM structure of SARS-CoV-2 BA.1 spike protein in complex with three-nAb 8H12, 3E2 and 1C4 Method: EM (single particle) / Resolution: 3.95 Å 62601 9kvt EMDB-62601, PDB-9kvt: Cryo-EM structure of SARS-CoV-2 BA.2 spike protein in complex with triple-nAb 8H12, 3E2 and 1C4 (local refinement) Method: EM (single particle) / Resolution: 3.9 Å 62620 9kwy EMDB-62620, PDB-9kwy: Cryo-EM structure of SARS-CoV-2 RBD in complex with ACE2 and mAb 1C4 Method: EM (single particle) / Resolution: 2.82 Å EMDB-65522: Cryo-EM structure of a 1C4 SpyTag-SpyCatcher mi3 nanoparticle Method: EM (single particle) / Resolution: 3.87 Å 65523 9w14 EMDB-65523, PDB-9w14: Cryo-EM structure of SARS-CoV-2 WT spike protein in complex with nAb 1C4 Method: EM (single particle) / Resolution: 2.33 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose
Source	mus musculus (house mouse) severe acute respiratory syndrome coronavirus 2 homo sapiens (human) Thermotoga maritima (bacteria)
Keywords	VIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / Neutralizing antibody / Cryo-EM / VIRAL PROTEIN-IMMUNE SYSTEM complex / VIRAL PROTEIN/HYDROLASE / VIRAL PROTEIN-HYDROLASE complex / VIRAL PROTEIN