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'''Unreleased structure'''


The entry 7f5h is ON HOLD
==The crystal structure of RBD-Nanobody complex, DL28 (SC4)==
<StructureSection load='7f5h' size='340' side='right'caption='[[7f5h]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7f5h]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2 Severe acute respiratory syndrome coronavirus 2] and [https://en.wikipedia.org/wiki/Vicugna_pacos Vicugna pacos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F5H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F5H FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7f5h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f5h OCA], [https://pdbe.org/7f5h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f5h RCSB], [https://www.ebi.ac.uk/pdbsum/7f5h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f5h ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== 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.


Authors: Luo, Z.P., Li, T., Lai, Y., Zhou, Y., Tan, J., Li, D.
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<ref>PMID:35722331</ref>


Description: The crystal structure of RBD-Nanobody complex, DL28 (SC4)
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Li, D]]
<div class="pdbe-citations 7f5h" style="background-color:#fffaf0;"></div>
[[Category: Luo, Z.P]]
 
[[Category: Lai, Y]]
==See Also==
[[Category: Li, T]]
*[[Antibody 3D structures|Antibody 3D structures]]
[[Category: Zhou, Y]]
== References ==
[[Category: Tan, J]]
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Severe acute respiratory syndrome coronavirus 2]]
[[Category: Vicugna pacos]]
[[Category: Lai Y]]
[[Category: Li D]]
[[Category: Li T]]
[[Category: Luo ZP]]
[[Category: Tan J]]
[[Category: Zhou Y]]
Retrieved from "https://proteopedia.org/7f5h"