8sph: Difference between revisions

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-'''Unreleased structure'''
-The entry 8sph is ON HOLD  until Paper Publication
+==Crystal structure of chimeric omicron RBD (strain XBB.1) complexed with human ACE2==
+<StructureSection load='8sph' size='340' side='right'caption='[[8sph]], [[Resolution|resolution]] 2.71&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8sph]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2 Severe acute respiratory syndrome coronavirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8SPH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8SPH 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]] 2.71&#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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=8sph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8sph OCA], [https://pdbe.org/8sph PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8sph RCSB], [https://www.ebi.ac.uk/pdbsum/8sph PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8sph ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ACE2_HUMAN ACE2_HUMAN] Carboxypeptidase which converts angiotensin I to angiotensin 1-9, a peptide of unknown function, and angiotensin II to angiotensin 1-7, a vasodilator. Also able to hydrolyze apelin-13 and dynorphin-13 with high efficiency. May be an important regulator of heart function. In case of human coronaviruses SARS and HCoV-NL63 infections, serve as functional receptor for the spike glycoprotein of both coronaviruses.<ref>PMID:10969042</ref> <ref>PMID:10924499</ref> <ref>PMID:14647384</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Understanding the evolutionary strategies of the SARS-CoV-2 omicron variant is crucial for comprehending the COVID-19 pandemic and preventing future coronavirus pandemics. In this study, we determined the crystal structures of the receptor-binding domains (RBDs) from currently circulating omicron subvariants XBB.1 and XBB.1.5 (also the emerging XBB.1.9.1), each complexed with human ACE2. We studied how individual RBD residues evolved structurally in omicron subvariants, specifically how they adapted to human ACE2. Our findings revealed that residues 493 and 496, which exhibited good human ACE2 adaptation in pre-omicron variants, evolved to poor adaptation in early omicron subvariants (but with good adaption to mouse ACE2) and then reverted to good adaptation in recent omicron subvariants. This result is consistent with the hypothesis that non-human animals facilitated the evolution of early omicron subvariants. Additionally, residue 486, which exhibited good human ACE2 adaptation in early omicron subvariants, evolved to poor adaptation in later omicron subvariants and then returned to good adaptation in recent omicron subvariants. This result is consistent with the hypothesis that immune evasion facilitated the evolution of later omicron subvariants. Thus, our study suggests that both non-human animals and immune evasion may have contributed to driving omicron evolution at different stages of the pandemic. IMPORTANCE The sudden emergence and continued evolution of the SARS-CoV-2 omicron variant have left many mysteries unanswered, such as the origin of early omicron subvariants and the factors driving omicron evolution. To address these questions, we studied the crystal structures of human ACE2-bound receptor-binding domains (RBDs) from omicron subvariants XBB.1 and XBB.1.5 (XBB.1.9.1). Our in-depth structural analysis sheds light on how specific RBD mutations adapt to either human or mouse ACE2 and suggests non-human animals and immune evasion may have influenced omicron evolution during different stages of the pandemic. These findings provide valuable insights into the mechanisms underlying omicron evolution, deepen our understanding of the COVID-19 pandemic, and have significant implications for preventing future coronavirus pandemics.
-Authors:
+Structural evolution of SARS-CoV-2 omicron in human receptor recognition.,Zhang W, Shi K, Geng Q, Herbst M, Wang M, Huang L, Bu F, Liu B, Aihara H, Li F J Virol. 2023 Aug 31;97(8):e0082223. doi: 10.1128/jvi.00822-23. Epub 2023 Aug 14. PMID:37578233<ref>PMID:37578233</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 8sph" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Spike protein 3D structures|Spike protein 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Severe acute respiratory syndrome coronavirus 2]]
+[[Category: Aihara H]]
+[[Category: Li F]]
+[[Category: Shi K]]
+[[Category: Zhang W]]