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	Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction.
Journal, issue, pages	J Biol Chem, Vol. 297, Issue 4, Page 101202, Year 2021
Publish date	Sep 16, 2021
Authors	Javeed Ahmad / Jiansheng Jiang / Lisa F Boyd / Allison Zeher / Rick Huang / Di Xia / Kannan Natarajan / David H Margulies /
PubMed Abstract	Combating the worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the emergence of new variants demands understanding of the structural basis of the interaction of ...Combating the worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the emergence of new variants demands understanding of the structural basis of the interaction of antibodies with the SARS-CoV-2 receptor-binding domain (RBD). Here, we report five X-ray crystal structures of sybodies (synthetic nanobodies) including those of binary and ternary complexes of Sb16-RBD, Sb45-RBD, Sb14-RBD-Sb68, and Sb45-RBD-Sb68, as well as unliganded Sb16. These structures reveal that Sb14, Sb16, and Sb45 bind the RBD at the angiotensin-converting enzyme 2 interface and that the Sb16 interaction is accompanied by a large conformational adjustment of complementarity-determining region 2. In contrast, Sb68 interacts at the periphery of the SARS-CoV-2 RBD-angiotensin-converting enzyme 2 interface. We also determined cryo-EM structures of Sb45 bound to the SARS-CoV-2 spike protein. Superposition of the X-ray structures of sybodies onto the trimeric spike protein cryo-EM map indicates that some sybodies may bind in both "up" and "down" configurations, but others may not. Differences in sybody recognition of several recently identified RBD variants are explained by these structures.
External links	J Biol Chem / PubMed:34537245 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.7 - 3.34 Å
Structure data	24105 7n0g EMDB-24105, PDB-7n0g: CryoEm structure of SARS-CoV-2 spike protein (S-6P, 1-up) in complex with sybodies (Sb45) Method: EM (single particle) / Resolution: 3.02 Å 24106 7n0h EMDB-24106, PDB-7n0h: CryoEM structure of SARS-CoV-2 spike protein (S-6P, 2-up) in complex with sybodies (Sb45) Method: EM (single particle) / Resolution: 3.34 Å PDB-7kgj: Crystal structure of synthetic nanobody (Sb45) complexes with SARS-CoV-2 receptor binding domain Method: X-RAY DIFFRACTION / Resolution: 2.3 Å PDB-7kgk: Crystal structure of synthetic nanobody (Sb16) complexes with SARS-CoV-2 receptor binding domain Method: X-RAY DIFFRACTION / Resolution: 2.6 Å PDB-7klw: Crystal structure of synthetic nanobody (Sb45+Sb68) complexes with SARS-CoV-2 receptor binding domain Method: X-RAY DIFFRACTION / Resolution: 2.6 Å PDB-7mfu: Crystal structure of synthetic nanobody (Sb14+Sb68) complexes with SARS-CoV-2 receptor binding domain Method: X-RAY DIFFRACTION / Resolution: 1.7 Å PDB-7mfv: Crystal structure of synthetic nanobody (Sb16) Method: X-RAY DIFFRACTION / Resolution: 1.9 Å
Chemicals	ChemComp-HOH: WATER ChemComp-EDO: 1,2-ETHANEDIOL ChemComp-GOL: GLYCEROL ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose
Source	synthetic construct (others) severe acute respiratory syndrome coronavirus 2
Keywords	VIRAL PROTEIN / SARS-CoV-2 / Spike Protein / RBD / Antibody / Nanobody / Sybody / epitopes / neutralization / Epitope / Receptor Binding Domain / Complex / IMMUNE SYSTEM / S-6P (HexaPro) / Sb45