9up9: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 9up9 is ~~ON HOLD~~

==Cystal Structure of Shark VNAR Nanobody==

== Structural highlights ==

<table><tr><td colspan='2'>[[9up9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chiloscyllium_plagiosum Chiloscyllium plagiosum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9UP9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9UP9 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]] 2Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=9up9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9up9 OCA], [https://pdbe.org/9up9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9up9 RCSB], [https://www.ebi.ac.uk/pdbsum/9up9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9up9 ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

Conventional antibodies are among the most frequently used and effective biological tools explored for therapeutic and diagnostic applications. However, they face significant limitations when it comes to challenges that demand specialized attributes such as rapid tissue penetration, the ability to bind to concealed epitopes, and stability in non-physiological environments. In recent years, shark-derived immunoglobulin variable new antigen receptor (vNAR) has emerged as a promising alternative to overcome these limitations. In this study, we constructed a naive vNAR phage display library from a white-spotted bamboo shark (Chiloscyllium plagiosum), with a library diversity size of approximately 3 x 10(11) clones. Next generation sequencing analysis revealed the high diversity of the library, allowing it to encompass a broad range of classical functional vNAR types. To confirm the usability of the library for the successful isolation of positive clones, we screened the library against wide range of antigens (n=9;) from different origin that includes viral, cancer, autoimmune, toxins, parasite, algae and plant antigens. We achieved a hit rate of approximately 100%, of potent binders with micro to nanomolar range affinity. The total number of unique binder's clones varied from 30%-100%, depending on the antigens and screening strategy. Furthermore, we provide an in-depth structural analysis by using X-ray crystallography of class IV vNARs from bamboo sharks, that remain underexplored. Our study represents a significant step forward in the field of single-domain antibody research and development.

~~Authors~~:

A high diversity naive variable new antigen receptor, vNAR, phage library for rapid nanobody discovery across diverse antigens.,Kumar V, Jangid K, Santhosh B, Dixit R, Yadav U, Verma S, Rout A, Surya S, Das M, Gupta R, Saroj A, Madhukalya R, Gupta M, Kalra M, Iqbal H, Kumar D, Sinha S, Tomar S, Kumar P, Kumar R J Biol Chem. 2025 Dec 22:111083. doi: 10.1016/j.jbc.2025.111083. PMID:41443416<ref>PMID:41443416</ref>

~~Description~~:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Chiloscyllium plagiosum]]

[[Category: Large Structures]]

[[Category: Jangid K]]

[[Category: Kumar P]]

[[Category: Kumar R]]

[[Category: Kumar V]]

[[Category: Tomar S]]

[[Category: Yadav U]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9up9 is ON HOLD
+==Cystal Structure of Shark VNAR Nanobody==
+<StructureSection load='9up9' size='340' side='right'caption='[[9up9]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9up9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chiloscyllium_plagiosum Chiloscyllium plagiosum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9UP9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9UP9 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=EDO:1,2-ETHANEDIOL'>EDO</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=9up9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9up9 OCA], [https://pdbe.org/9up9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9up9 RCSB], [https://www.ebi.ac.uk/pdbsum/9up9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9up9 ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Conventional antibodies are among the most frequently used and effective biological tools explored for therapeutic and diagnostic applications. However, they face significant limitations when it comes to challenges that demand specialized attributes such as rapid tissue penetration, the ability to bind to concealed epitopes, and stability in non-physiological environments. In recent years, shark-derived immunoglobulin variable new antigen receptor (vNAR) has emerged as a promising alternative to overcome these limitations. In this study, we constructed a naive vNAR phage display library from a white-spotted bamboo shark (Chiloscyllium plagiosum), with a library diversity size of approximately 3 x 10(11) clones. Next generation sequencing analysis revealed the high diversity of the library, allowing it to encompass a broad range of classical functional vNAR types. To confirm the usability of the library for the successful isolation of positive clones, we screened the library against wide range of antigens (n=9;) from different origin that includes viral, cancer, autoimmune, toxins, parasite, algae and plant antigens. We achieved a hit rate of approximately 100%, of potent binders with micro to nanomolar range affinity. The total number of unique binder's clones varied from 30%-100%, depending on the antigens and screening strategy. Furthermore, we provide an in-depth structural analysis by using X-ray crystallography of class IV vNARs from bamboo sharks, that remain underexplored. Our study represents a significant step forward in the field of single-domain antibody research and development.
-Authors:
+A high diversity naive variable new antigen receptor, vNAR, phage library for rapid nanobody discovery across diverse antigens.,Kumar V, Jangid K, Santhosh B, Dixit R, Yadav U, Verma S, Rout A, Surya S, Das M, Gupta R, Saroj A, Madhukalya R, Gupta M, Kalra M, Iqbal H, Kumar D, Sinha S, Tomar S, Kumar P, Kumar R J Biol Chem. 2025 Dec 22:111083. doi: 10.1016/j.jbc.2025.111083. PMID:41443416<ref>PMID:41443416</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 9up9" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Chiloscyllium plagiosum]]
+[[Category: Large Structures]]
+[[Category: Jangid K]]
+[[Category: Kumar P]]
+[[Category: Kumar R]]
+[[Category: Kumar V]]
+[[Category: Tomar S]]
+[[Category: Yadav U]]