7f5h | pdb_00007f5h

The crystal structure of RBD-Nanobody complex, DL28 (SC4)

spinqualitylabelsall models 7f5h, resolution 3.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7f5h is a 4 chain structure with sequence from Severe acute respiratory syndrome coronavirus 2 and Vicugna pacos. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 3Å Ligands: BMA, FUC, GOL, NAG, PO4 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed SARS-CoV-2 and its variants, such as the Omicron continue to threaten public health. The virus recognizes the host cell by attaching its Spike (S) receptor-binding domain (RBD) to the host receptor, ACE2. Therefore, RBD is a primary target for neutralizing antibodies and vaccines. Here, we report the isolation and biological and structural characterization of a single-chain antibody (nanobody) from RBD-immunized alpaca. The nanobody, named DL28, binds to RBD tightly with a K (D) of 1.56 nM and neutralizes the original SARS-CoV-2 strain with an IC(50) of 0.41 mug mL(-1). Neutralization assays with a panel of variants of concern (VOCs) reveal its wide-spectrum activity with IC(50) values ranging from 0.35 to 1.66 mug mL(-1) for the Alpha/Beta/Gamma/Delta and an IC(50) of 0.66 mug mL(-1) for the currently prevalent Omicron. Competition binding assays show that DL28 blocks ACE2-binding. However, structural characterizations and mutagenesis suggest that unlike most antibodies, the blockage by DL28 does not involve direct competition or steric hindrance. Rather, DL28 may use a "conformation competition" mechanism where it excludes ACE2 by keeping an RBD loop in a conformation incompatible with ACE2-binding. Structural Characterization of a Neutralizing Nanobody With Broad Activity Against SARS-CoV-2 Variants.,Li T, Zhou B, Luo Z, Lai Y, Huang S, Zhou Y, Li Y, Gautam A, Bourgeau S, Wang S, Bao J, Tan J, Lavillette D, Li D Front Microbiol. 2022 Jun 2;13:875840. doi: 10.3389/fmicb.2022.875840. , eCollection 2022. PMID:35722331 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Antibody 3D structures

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