View source for 8zfv


==Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2 in complex with ceftriaxone==
<StructureSection load='8zfv' size='340' side='right'caption='[[8zfv]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8zfv]] 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]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8ZFV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8ZFV 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&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9F2:(7~{R})-7-[[2-(2-azanyl-1,3-thiazol-4-yl)-2-methoxyimino-ethanoyl]amino]-3-[[2-methyl-5,6-bis(oxidanylidene)-1~{H}-1,2,4-triazin-3-yl]sulfanylmethyl]-8-oxidanylidene-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic+acid'>9F2</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=8zfv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8zfv OCA], [https://pdbe.org/8zfv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8zfv RCSB], [https://www.ebi.ac.uk/pdbsum/8zfv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8zfv ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NCAP_SARS2 NCAP_SARS2] Packages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP) and plays a fundamental role during virion assembly through its interactions with the viral genome and membrane protein M. Plays an important role in enhancing the efficiency of subgenomic viral RNA transcription as well as viral replication.
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== Publication Abstract from PubMed ==
The SARS-CoV-2 nucleocapsid (N) protein is an essential structural element of the virion, playing a crucial role in enclosing the viral genome into a ribonucleoprotein (RNP) assembly, as well as viral replication and transmission. The C-terminal domain of the N-protein (N-CTD) is essential for encapsidation, contributing to the stabilization of the RNP complex. In a previous study, three inhibitors (ceftriaxone, cefuroxime, and ampicillin) were screened for their potential to disrupt the RNA packaging process by targeting the N-protein. However, the binding efficacy, mechanism of RNA binding inhibition, and molecular insights of binding with N-CTD remain unclear. In this study, we evaluated the binding efficacy of these inhibitors using isothermal titration calorimetry (ITC), revealing the affinity of ceftriaxone (18 +/- 1.3 muM), cefuroxime (55 +/- 4.2 muM), and ampicillin (28 +/- 1.2 muM) with the N-CTD. Further inhibition assay and fluorescence polarisation assay demonstrated RNA binding inhibition, with IC(50) ranging from approximately 12 to 18 muM and K(D) values between 24 muM to 32 muM for the inhibitors, respectively. Additionally, we also determined the inhibitor-bound complex crystal structures of N-CTD-Ceftriaxone (2.0 A) and N-CTD-Ampicillin (2.2 A), along with the structure of apo N-CTD (1.4 A). These crystal structures revealed previously unobserved interaction sites involving residues K261, K266, R293, Q294, and W301 at the oligomerization interface and the predicted RNA-binding region of N-CTD. These findings provide valuable molecular insights into the inhibition of N-CTD, highlighting its potential as an underexplored but promising target for the development of novel antiviral agents against coronaviruses.

Structural insights into the RNA binding inhibitors of the C-terminal domain of the SARS-CoV-2 nucleocapsid.,Dhaka P, Mahto JK, Singh A, Kumar P, Tomar S J Struct Biol. 2025 Mar 18;217(2):108197. doi: 10.1016/j.jsb.2025.108197. PMID:40113149<ref>PMID:40113149</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8zfv" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Severe acute respiratory syndrome coronavirus 2]]
[[Category: Dhaka P]]
[[Category: Kumar P]]
[[Category: Mahto JK]]
[[Category: Tomar S]]