View source for 7cqd


==The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA14 tag inserted between the residues 235 and 236==
<StructureSection load='7cqd' size='340' side='right'caption='[[7cqd]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7cqd]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5], [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CQD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CQD 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]] 3.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</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=7cqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cqd OCA], [https://pdbe.org/7cqd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cqd RCSB], [https://www.ebi.ac.uk/pdbsum/7cqd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cqd ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Y1964_AQUAE Y1964_AQUAE] [https://www.uniprot.org/uniprot/PDPN_HUMAN PDPN_HUMAN] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Antibody labeling has been conducted extensively for structure determination using both X-ray crystallography and electron microscopy (EM). However, establishing target-specific antibodies is a prerequisite for applying antibody-assisted structural analysis. To expand the applicability of this strategy, an alternative method has been developed to prepare an antibody complex by inserting an exogenous epitope into the target. It has already been demonstrated that the Fab of the NZ-1 monoclonal antibody can form a stable complex with a target containing a PA12 tag as an inserted epitope. Nevertheless, it was also found that complex formation through the inserted PA12 tag inevitably caused structural changes around the insertion site on the target. Here, an attempt was made to improve the tag-insertion method, and it was consequently discovered that an alternate tag (PA14) could replace various loops on the target without inducing large structural changes. Crystallographic analysis demonstrated that the inserted PA14 tag adopts a loop-like conformation with closed ends in the antigen-binding pocket of the NZ-1 Fab. Due to proximity of the termini in the bound conformation, the more optimal PA14 tag had only a minor impact on the target structure. In fact, the PA14 tag could also be inserted into a sterically hindered loop for labeling. Molecular-dynamics simulations also showed a rigid structure for the target regardless of PA14 insertion and complex formation with the NZ-1 Fab. Using this improved labeling technique, negative-stain EM was performed on a bacterial site-2 protease, which enabled an approximation of the domain arrangement based on the docking mode of the NZ-1 Fab.

Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion.,Tamura-Sakaguchi R, Aruga R, Hirose M, Ekimoto T, Miyake T, Hizukuri Y, Oi R, Kaneko MK, Kato Y, Akiyama Y, Ikeguchi M, Iwasaki K, Nogi T Acta Crystallogr D Struct Biol. 2021 May 1;77(Pt 5):645-662. doi: , 10.1107/S2059798321002527. Epub 2021 Apr 19. PMID:33950020<ref>PMID:33950020</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7cqd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Aquifex aeolicus VF5]]
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Rattus norvegicus]]
[[Category: Aruga R]]
[[Category: Nogi T]]
[[Category: Tamura-Sakaguchi R]]