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 structural and mechanistic atlas of NTD antibody neutralization and immune escape across SARS-CoV-2 prototype and its (sub-)variants.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 123, Issue 32, Page e2535385123, Year 2026
Publish date	Aug 11, 2026
Authors	Jianjie Zhou / Wenyu Li / Xiaoyun Wang / Junqing Sun / Shuxin Guo / Xiaoyu Rong / Zhou Tong / Lianpan Dai / William Jun Liu / Jianxun Qi / George Fu Gao / Qihui Wang /
PubMed Abstract	The N-terminal domain (NTD) of the SARS-CoV-2 spike (S) is a critical antibody target, yet its epitope organization, neutralization mechanisms, and immune evasion strategies remain incompletely ...The N-terminal domain (NTD) of the SARS-CoV-2 spike (S) is a critical antibody target, yet its epitope organization, neutralization mechanisms, and immune evasion strategies remain incompletely resolved. Here, we classify NTD antibodies into nine spatially distinct classes (designated as NTD-1 to NTD-9), including a cryptic epitope defined here (NTD-8). Mechanistic studies reveal that NTD-5 and NTD-9 antibodies neutralize by inducing S1 shedding, thereby extending this mechanism to selected NTD-directed antibodies. Format profiling shows that while most NTD antibodies require bivalency, selected antibodies from NTD-3, NTD-5, and NTD-9 retain neutralizing activity in Fab form. Profiling 41 antibodies across prototype, Delta, and 17 Omicron subvariants defines an epitope-resolved escape landscape and enables dissection of three convergent evasion strategies: contact residue disruption, glycan shielding, and conformational remodeling. Notably, the KP.3.1.1 subvariant uses a dual escape mechanism in which ∆S31 introduces N30 glycosylation and substantially remodels the S27-R34 region, undermining recognition by both NTD-5 and NTD-9 antibodies. These findings provide a structural and mechanistic framework for rational vaccine and antibody design resilient to antigenic drift.
External links	Proc Natl Acad Sci U S A / PubMed:42555640 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.52 - 3.93 Å
Structure data	65704 9w6u EMDB-65704, PDB-9w6u: Structure of the PT NTD-C1554-C1540 complex Method: EM (single particle) / Resolution: 2.81 Å 65993 9wig EMDB-65993, PDB-9wig: Structure of the PT NTD-C1536-CoV2-3434-BLN8 complex Method: EM (single particle) / Resolution: 3.93 Å PDB-9x9z: Structure of the Omicron BA.2.86 variant Spike N-terminal domain(NTD)in complex with the antibody Fab fragment, C1717 Method: X-RAY DIFFRACTION / Resolution: 2.55 Å PDB-9xa0: Structure of the Omicron KP.3.1.1 variant Spike N-terminal domain(NTD)in complex with the C1717 Fab and S2L20 Fab Method: X-RAY DIFFRACTION / Resolution: 3.51 Å PDB-9xa4: Structure of the Omicron BA.4/5 Spike N-terminal domain(NTD) in complex with the AC2 Fab Method: X-RAY DIFFRACTION / Resolution: 2.52 Å PDB-9xa5: Structure of the Omicron BA.4/5 Spike N-terminal domain(NTD) in complex with the AC8 Fab Method: X-RAY DIFFRACTION / Resolution: 3.32 Å PDB-9xar: Structure of the SARS-CoV-2 Spike N-terminal domain(NTD) in complex with the C1624 Fab Method: X-RAY DIFFRACTION / Resolution: 2.77 Å PDB-9xaw: Structure of the SARS-CoV-2 Spike N-terminal domain(NTD) in complex with the BLN8 Fab Method: X-RAY DIFFRACTION / Resolution: 3.13 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose ChemComp-HOH: WATER ChemComp-EDO: 1,2-ETHANEDIOL
Source	severe acute respiratory syndrome coronavirus 2 homo sapiens (human)
Keywords	VIRAL PROTEIN/PROTEIN BINDING / PT NTD / C1554-C1540 / PROTEIN BINDING/VIRAL PROTEIN / VIRAL PROTEIN-PROTEIN BINDING complex / FAB / IMMUNE SYSTEM / Complex