6al0: Difference between revisions
New page: '''Unreleased structure''' The entry 6al0 is ON HOLD Authors: Tamura, R., Oi, R., Kaneko, M.K., Kato, Y., Nogi, T. Description: tag-inserted PDZ tandem in complex with Fab [[Category: ... |
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The | ==The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA12 tag inserted between the residues 263 and 267== | ||
<StructureSection load='6al0' size='340' side='right'caption='[[6al0]], [[Resolution|resolution]] 2.60Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6al0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5] 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=6AL0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AL0 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]] 2.6Å</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>, <scene name='pdbligand=SNN:L-3-AMINOSUCCINIMIDE'>SNN</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=6al0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6al0 OCA], [https://pdbe.org/6al0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6al0 RCSB], [https://www.ebi.ac.uk/pdbsum/6al0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6al0 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Y1964_AQUAE Y1964_AQUAE] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
An antibody fragment that recognizes the tertiary structure of a target protein with high affinity can be utilized as a crystallization chaperone. Difficulties in establishing conformation-specific antibodies, however, limit the applicability of antibody fragment-assisted crystallization. Here, we attempted to establish an alternative method to promote the crystallization of target proteins using an already established anti-tag antibody. The monoclonal antibody NZ-1 recognizes the PA tag with an extremely high affinity. It was also established that the PA tag is accommodated in the antigen-binding pocket in a bent conformation, compatible with an insertion into loop regions on the target. We, therefore, explored the application of NZ-1 Fab as a crystallization chaperone that complexes with a target protein displaying a PA tag. Specifically, we inserted the PA tag into the beta-hairpins of the PDZ tandem fragment of a bacterial Site-2 protease. We crystallized the PA-inserted PDZ tandem mutants with the NZ-1 Fab and solved the co-crystal structure to analyze their interaction modes. Although the initial insertion designs produced only moderate-resolution structures, eliminating the solvent-accessible space between the NZ-1 Fab and target PDZ tandem improved the diffraction qualities remarkably. Our results demonstrate that the NZ-1-PA system efficiently promotes crystallization of the target protein. The present work also suggests that beta-hairpins are suitable sites for the PA insertion because the PA tag contains a Pro-Gly sequence with a propensity for a beta-turn conformation. | |||
Application of the NZ-1 Fab as a crystallization chaperone for PA tag-inserted target proteins.,Tamura R, Oi R, Akashi S, Kaneko MK, Kato Y, Nogi T Protein Sci. 2019 Jan 21. doi: 10.1002/pro.3580. PMID:30666745<ref>PMID:30666745</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6al0" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: Kato | ==See Also== | ||
[[Category: | *[[Antibody 3D structures|Antibody 3D structures]] | ||
[[Category: Tamura | == References == | ||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Aquifex aeolicus VF5]] | |||
[[Category: Large Structures]] | |||
[[Category: Rattus norvegicus]] | |||
[[Category: Kaneko MK]] | |||
[[Category: Kato Y]] | |||
[[Category: Nogi T]] | |||
[[Category: Oi R]] | |||
[[Category: Tamura R]] | |||
Latest revision as of 13:09, 15 November 2023
The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA12 tag inserted between the residues 263 and 267The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA12 tag inserted between the residues 263 and 267
Structural highlights
FunctionPublication Abstract from PubMedAn antibody fragment that recognizes the tertiary structure of a target protein with high affinity can be utilized as a crystallization chaperone. Difficulties in establishing conformation-specific antibodies, however, limit the applicability of antibody fragment-assisted crystallization. Here, we attempted to establish an alternative method to promote the crystallization of target proteins using an already established anti-tag antibody. The monoclonal antibody NZ-1 recognizes the PA tag with an extremely high affinity. It was also established that the PA tag is accommodated in the antigen-binding pocket in a bent conformation, compatible with an insertion into loop regions on the target. We, therefore, explored the application of NZ-1 Fab as a crystallization chaperone that complexes with a target protein displaying a PA tag. Specifically, we inserted the PA tag into the beta-hairpins of the PDZ tandem fragment of a bacterial Site-2 protease. We crystallized the PA-inserted PDZ tandem mutants with the NZ-1 Fab and solved the co-crystal structure to analyze their interaction modes. Although the initial insertion designs produced only moderate-resolution structures, eliminating the solvent-accessible space between the NZ-1 Fab and target PDZ tandem improved the diffraction qualities remarkably. Our results demonstrate that the NZ-1-PA system efficiently promotes crystallization of the target protein. The present work also suggests that beta-hairpins are suitable sites for the PA insertion because the PA tag contains a Pro-Gly sequence with a propensity for a beta-turn conformation. Application of the NZ-1 Fab as a crystallization chaperone for PA tag-inserted target proteins.,Tamura R, Oi R, Akashi S, Kaneko MK, Kato Y, Nogi T Protein Sci. 2019 Jan 21. doi: 10.1002/pro.3580. PMID:30666745[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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