9s60: Difference between revisions

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'''Unreleased structure'''


The entry 9s60 is ON HOLD  until Paper Publication
==Structural and proteomics analysis of the mouse cathepsin B - DARPin 4m3 complex reveals determinants of species - specific binding==
<StructureSection load='9s60' size='340' side='right'caption='[[9s60]], [[Resolution|resolution]] 1.69&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9s60]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9S60 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9S60 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]] 1.69&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</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=9s60 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9s60 OCA], [https://pdbe.org/9s60 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9s60 RCSB], [https://www.ebi.ac.uk/pdbsum/9s60 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9s60 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CATB_MOUSE CATB_MOUSE] Thiol protease which is believed to participate in intracellular degradation and turnover of proteins (By similarity). Cleaves matrix extracellular phosphoglycoprotein MEPE (By similarity). Involved in the solubilization of cross-linked TG/thyroglobulin in the thyroid follicle lumen (PubMed:12782676). Has also been implicated in tumor invasion and metastasis (By similarity).[UniProtKB:P07858]<ref>PMID:12782676</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Cathepsin B (CatB) is a lysosomal cysteine protease that plays a major role in various pathologies and is therefore considered a valuable therapeutic target. To address species-specific inhibitor challenges, we characterized the selective binding of designed ankyrin repeat protein (DARPin) 4m3 toward mouse cathepsin B (mCatB) over human CatB (hCatB). The mCatB-DARPin 4m3 complex was validated by size-exclusion chromatography (SEC), nano-differential scanning fluorimetry (nano-DSF), and surface plasmon resonance (SPR), revealing high affinity binding (K(D) = 65.7 nM) and potent inhibition (Ki = 26.7 nM; mixed competitive/noncompetitive). DARPin 4m3 showed no binding/inhibition toward hCatB. The 1.67 A crystal structure of the complex-the first for mCatB-identified key interaction residues (e.g., I65/Q66 in mCatB vs. S65/M66 in hCatB) conferring selectivity. Proteomic analysis of endogenous substrates using a support vector machine (SVM) revealed greater similarity between mCatB and hCatB cleavages (Area Under the Curve (AUC) = 0.733) than between mCatB and other human cathepsins (AUC = 0.939-0.965). Clustering and SVM methods offer broadly applicable tools for protease specificity profiling in drug discovery. This study demonstrates the utility of DARPins for species-selective targeting and highlights the importance of integrated structural and proteomic approaches for dissecting protein-protein interactions.


Authors: Tusar, L., Zaric, M., Usenik, A., Vasiljeva, O., Novak, M., Turk, D., Turk, B.
Structural and Proteomic Analysis of the Mouse Cathepsin B-DARPin 4m3 Complex Reveals Species-Specific Binding Determinants.,Zaric M, Tusar L, Kramer L, Vasiljeva O, Novak M, Impens F, Usenik A, Gevaert K, Turk D, Turk B Int J Mol Sci. 2025 Dec 10;26(24):11910. doi: 10.3390/ijms262411910. PMID:41465336<ref>PMID:41465336</ref>


Description: Structural and proteomics analysis of the mouse cathepsin B -DARPin 4m3 complex reveals determinants of species -specific binding
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Novak, M]]
<div class="pdbe-citations 9s60" style="background-color:#fffaf0;"></div>
[[Category: Turk, D]]
== References ==
[[Category: Turk, B]]
<references/>
[[Category: Tusar, L]]
__TOC__
[[Category: Zaric, M]]
</StructureSection>
[[Category: Vasiljeva, O]]
[[Category: Large Structures]]
[[Category: Usenik, A]]
[[Category: Mus musculus]]
[[Category: Synthetic construct]]
[[Category: Novak M]]
[[Category: Turk B]]
[[Category: Turk D]]
[[Category: Tusar L]]
[[Category: Usenik A]]
[[Category: Vasiljeva O]]
[[Category: Zaric M]]
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