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	Superimmunity by pan-sarbecovirus nanobodies.
Journal, issue, pages	Cell Rep, Vol. 39, Issue 13, Page 111004, Year 2022
Publish date	Jun 28, 2022
Authors	Yufei Xiang / Wei Huang / Hejun Liu / Zhe Sang / Sham Nambulli / Jérôme Tubiana / Kevin L Williams / W Paul Duprex / Dina Schneidman-Duhovny / Ian A Wilson / Derek J Taylor / Yi Shi /
PubMed Abstract	Vaccine boosters and infection can facilitate the development of SARS-CoV-2 antibodies with improved potency and breadth. Here, we observe superimmunity in a camelid extensively immunized with the ...Vaccine boosters and infection can facilitate the development of SARS-CoV-2 antibodies with improved potency and breadth. Here, we observe superimmunity in a camelid extensively immunized with the SARS-CoV-2 receptor-binding domain (RBD). We rapidly isolate a large repertoire of specific ultra-high-affinity nanobodies that bind strongly to all known sarbecovirus clades using integrative proteomics. These pan-sarbecovirus nanobodies (psNbs) are highly effective against SARS-CoV and SARS-CoV-2 variants, including Omicron, with the best median neutralization potency at single-digit nanograms per milliliter. A highly potent, inhalable, and bispecific psNb (PiN-31) is also developed. Structural determinations of 13 psNbs with the SARS-CoV-2 spike or RBD reveal five epitope classes, providing insights into the mechanisms and evolution of their broad activities. The highly evolved psNbs target small, flat, and flexible epitopes that contain over 75% of conserved RBD surface residues. Their potencies are strongly and negatively correlated with the distance of the epitopes from the receptor binding sites.
External links	Cell Rep / PubMed:35738279 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.71 - 3.6 Å
Structure data	27061 8cxn EMDB-27061, PDB-8cxn: SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-57 Method: EM (single particle) / Resolution: 2.9 Å 27067 8cxq EMDB-27067, PDB-8cxq: SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-22 Method: EM (single particle) / Resolution: 2.3 Å 27068 8cy6 EMDB-27068, PDB-8cy6: SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-65 Method: EM (single particle) / Resolution: 3.2 Å 27069 8cy7 EMDB-27069, PDB-8cy7: SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-34 Method: EM (single particle) / Resolution: 2.9 Å 27071 8cy9 EMDB-27071, PDB-8cy9: SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-23 Method: EM (single particle) / Resolution: 2.9 Å 27072 8cya EMDB-27072, PDB-8cya: SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-67 Method: EM (single particle) / Resolution: 2.7 Å 27073 8cyb EMDB-27073, PDB-8cyb: SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-8 Method: EM (single particle) / Resolution: 2.7 Å 27074 8cyc EMDB-27074, PDB-8cyc: SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-34 Method: EM (single particle) / Resolution: 2.9 Å 27075 8cyd EMDB-27075, PDB-8cyd: SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-45 Method: EM (single particle) / Resolution: 2.6 Å 27080 8cyj EMDB-27080, PDB-8cyj: RBD of SARS-CoV-2 Spike protein in complex with pan-sarbecovirus nanobodies 2-10, 2-67, 2-62 and 1-25 Method: EM (single particle) / Resolution: 3.6 Å PDB-8cwu: Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a cross-neutralizing nanobody 1-21 Method: X-RAY DIFFRACTION / Resolution: 1.71 Å PDB-8cwv: Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a cross-neutralizing nanobody 2-31 and a human antibody CC12.1 Fab Method: X-RAY DIFFRACTION / Resolution: 2.51 Å
Chemicals	ChemComp-HOH: WATER / Water ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine ChemComp-AH2: 1-deoxy-alpha-D-mannopyranose
Source	lama glama (llama) severe acute respiratory syndrome coronavirus 2 homo sapiens (human)
Keywords	IMMUNE SYSTEM / cross-neutralizing antibody; nanobody; SARS-CoV-2; Sarbecovirus; IMMUNE SYSTEM; VHH / cross-neutralizing antibody; nanobody; SARS-CoV-2; Sarbecovirus; IMMUNE SYSTEM; VHH; CC12.1 / VIRAL PROTEIN / SARS-CoV-2 / Spike protein / nanobody / broad binding