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	Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein and potentially drive the genesis of Omicron variants.
Journal, issue, pages	Nat Commun, Vol. 15, Issue 1, Page 7585, Year 2024
Publish date	Aug 31, 2024
Authors	Qihong Yan / Xijie Gao / Banghui Liu / Ruitian Hou / Ping He / Yong Ma / Yudi Zhang / Yanjun Zhang / Zimu Li / Qiuluan Chen / Jingjing Wang / Xiaohan Huang / Huan Liang / Huiran Zheng / Yichen Yao / Xianying Chen / Xuefeng Niu / Jun He / Ling Chen / Jincun Zhao / Xiaoli Xiong /
PubMed Abstract	Continued evolution of SARS-CoV-2 generates variants to challenge antibody immunity established by infection and vaccination. A connection between population immunity and genesis of virus variants ...Continued evolution of SARS-CoV-2 generates variants to challenge antibody immunity established by infection and vaccination. A connection between population immunity and genesis of virus variants has long been suggested but its molecular basis remains poorly understood. Here, we identify a class of SARS-CoV-2 neutralizing public antibodies defined by their shared usage of VL6-57 light chains. Although heavy chains of diverse genotypes are utilized, convergent HCDR3 rearrangements have been observed among these public antibodies to cooperate with germline VL6-57 LCDRs to target a convergent epitope defined by RBD residues S371-S373-S375. Antibody repertoire analysis identifies that this class of VL6-57 antibodies is present in SARS-CoV-2-naive individuals and is clonally expanded in most COVID-19 patients. We confirm that Omicron-specific substitutions at S371, S373 and S375 mediate escape of antibodies of the VL6-57 class. These findings support that this class of public antibodies constitutes a potential immune pressure promoting the introduction of S371L/F-S373P-S375F in Omicron variants. The results provide further molecular evidence to support that antigenic evolution of SARS-CoV-2 is driven by antibody mediated population immunity.
External links	Nat Commun / PubMed:39217172 / PubMed Central
Methods	EM (single particle)
Resolution	3.16 - 8.45 Å
Structure data	60099 8zhd EMDB-60099, PDB-8zhd: SARS-CoV-2 spike trimer (6P) in complex with two R1-26 Fabs Method: EM (single particle) / Resolution: 3.41 Å 60100 8zhe EMDB-60100, PDB-8zhe: SARS-CoV-2 spike trimer (6P) in complex with three R1-26 Fabs Method: EM (single particle) / Resolution: 3.16 Å 60101 8zhf EMDB-60101, PDB-8zhf: SARS-CoV-2 spike trimer (6P) in complex with R1-26 Fab, head-to-head aggregate Method: EM (single particle) / Resolution: 5.26 Å 60102 8zhg EMDB-60102, PDB-8zhg: SARS-CoV-2 spike trimer (6P) in complex with R1-26 Fab, focused refinement of RBD-Fab region Method: EM (single particle) / Resolution: 3.51 Å 60103 8zhh EMDB-60103, PDB-8zhh: SARS-CoV-2 spike trimer (6P) in complex with two H18 Fabs Method: EM (single particle) / Resolution: 5.55 Å 60104 8zhi EMDB-60104, PDB-8zhi: SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs Method: EM (single particle) / Resolution: 6.05 Å 60105 8zhj EMDB-60105, PDB-8zhj: SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs, head-to-head aggregate (C1 symmetry) Method: EM (single particle) / Resolution: 8.45 Å 60106 8zhk EMDB-60106, PDB-8zhk: SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs, head-to-head aggregate (C3 symmetry) Method: EM (single particle) / Resolution: 6.3 Å 60107 8zhl EMDB-60107, PDB-8zhl: SARS-CoV-2 spike trimer (6P) in complex with two H18 and two R1-32 Fabs Method: EM (single particle) / Resolution: 3.96 Å 60108 8zhm EMDB-60108, PDB-8zhm: SARS-CoV-2 spike trimer (6P) in complex with three H18 and three R1-32 Fabs Method: EM (single particle) / Resolution: 3.39 Å 60109 8zhn EMDB-60109, PDB-8zhn: SARS-CoV-2 spike trimer (6P) in complex with three H18 and three R1-32 Fabs (one RBD rotated) Method: EM (single particle) / Resolution: 4.12 Å 60110 8zho EMDB-60110, PDB-8zho: SARS-CoV-2 S1 in complex with H18 and R1-32 Fab Method: EM (single particle) / Resolution: 3.54 Å 60111 8zhp EMDB-60111, PDB-8zhp: Dimer of SARS-CoV-2 S1 in complex with H18 and R1-32 Fabs Method: EM (single particle) / Resolution: 3.66 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose
Source	enterobacteria phage t6 (virus) homo sapiens (human) synthetic construct (others) severe acute respiratory syndrome coronavirus 2
Keywords	VIRAL PROTEIN/IMMUNE SYSTEM / Spike protein / RBD / Antibody / Fab / Viral protein / VIRAL PROTEIN-IMMUNE SYSTEM complex