9l08: Difference between revisions

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'''Unreleased structure'''


The entry 9l08 is ON HOLD  until Paper Publication
==Cyclic Trimer of Helix-Linked Cytochrome c555==
<StructureSection load='9l08' size='340' side='right'caption='[[9l08]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9l08]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9L08 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9L08 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]] 1.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</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=9l08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9l08 OCA], [https://pdbe.org/9l08 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9l08 RCSB], [https://www.ebi.ac.uk/pdbsum/9l08 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9l08 ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Protein-based supramolecules require precise arrangement of building blocks. A regular-triangle trimer (cp-c(555))(3) has been constructed using an alpha-helix-inserted-circular permutant (cp-c(555)) of Aquifex aeolicus cytochrome (cyt) c(555), where the trimers may dissociate to monomers. In this study, we stabilized the regular-triangle structure by constructing a cyclic regular-triangle of three alpha-helix-linked cyt c(555) molecules using sortase-mediated ligation (SML). Comparing SML using sortase A for six cp-c(555) variant trimers, the variant with GGG at the N-terminus and LPETG at the C-terminus reacted most efficiently. OP-(c(555))(3) was designed, in which two cyt c(555) molecules were fused using an alpha-helix, generating a dimer. The cyt c(555) C-terminal region was attached to the N-terminus of the dimer, and the cyt c(555) N-terminal region was attached to the C-terminus of the dimer using the same alpha-helix. OP-(c(555))(3) was expressed in Escherichia coli cells, and the termini were connected by SML, forming a cyclic regular-triangle, CL-(c(555))(3). CL-(c(555))(3) showed higher thermostability than (cp-c(555))(3) and OP-(c(555))(3). CL-(c(555))(3) structural stability was confirmed using high-speed atomic force microscopy. The X-ray crystal structure of CL-(c(555))(3) showed a cyclic structure and a nanoporous supramolecular assembly. These results demonstrate that a nanoporous supramolecular assembly can be constructed by designing a cyclic molecule with a central hole using SML.


Authors: Novientri, G., Mashima, T., Matsuura, H., Ogata, H., Hirota, S.
Construction of a Cyclic Regular-Triangle Trimer of Cytochrome c(555) with a Central Hole Using Sortase A.,Novientri G, Fujiwara K, Mashima T, Matsuura H, Ogata H, Uchihashi T, Fujii S, Sambongi Y, Hirota S Chemistry. 2025 May 14;31(27):e202404736. doi: 10.1002/chem.202404736. Epub 2025 , Apr 16. PMID:40148242<ref>PMID:40148242</ref>


Description: Cyclic Trimer of Helix-Linked Cytochrome c555
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Matsuura, H]]
<div class="pdbe-citations 9l08" style="background-color:#fffaf0;"></div>
[[Category: Novientri, G]]
== References ==
[[Category: Mashima, T]]
<references/>
[[Category: Ogata, H]]
__TOC__
[[Category: Hirota, S]]
</StructureSection>
[[Category: Aquifex aeolicus VF5]]
[[Category: Large Structures]]
[[Category: Hirota S]]
[[Category: Mashima T]]
[[Category: Matsuura H]]
[[Category: Novientri G]]
[[Category: Ogata H]]
Retrieved from "https://proteopedia.org/9l08"