5z25 - Revision history

OCA at 08:44, 22 November 2023

OCA — Wed, 22 Nov 2023 08:44:04 GMT

←Older revision		Revision as of 08:44, 22 November 2023
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	==Trimeric Alpha-Helix-Inserted Circular Permutant of Cytochrome c555==		==Trimeric Alpha-Helix-Inserted Circular Permutant of Cytochrome c555==
-	<StructureSection load='5z25' size='340' side='right' caption='[[5z25]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5z25' size='340' side='right'caption='[[5z25]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z25]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aquae Aquae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z25 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Z25 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z25]] is a 1 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=5Z25 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z25 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=HEC:HEME+C'>HEC</scene~~>, ~~<scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.7Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~cycB2, aq_1550 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=224324 AQUAE])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5z25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z25 OCA], [~~http~~://pdbe.org/5z25 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5z25 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5z25 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5z25 ProSAT]</span></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=5z25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z25 OCA], [https://pdbe.org/5z25 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z25 RCSB], [https://www.ebi.ac.uk/pdbsum/5z25 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z25 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O67504_AQUAE O67504_AQUAE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aquae~~]]	+	[[Category: Aquifex aeolicus VF5]]
-	[[Category: Higuchi, Y]]	+	[[Category: Large Structures]]
-	[[Category: Hirota, S]]	+	[[Category: Higuchi Y]]
-	[[Category: Nagao, S]]	+	[[Category: Hirota S]]
-	[[Category: Oda, A]]	+	[[Category: Nagao S]]
-	[[Category: Shibata, N]]	+	[[Category: Oda A]]
-	[[Category: Ueda, I]]	+	[[Category: Shibata N]]
-	[[Category: Yamanaka, M]]	+	[[Category: Ueda I]]
-	~~[[Category: Electron transport]]~~	+	[[Category: Yamanaka M]]
-	~~[[Category: Permutant~~]]	+

OCA at 07:08, 28 March 2018

OCA — Wed, 28 Mar 2018 07:08:56 GMT

←Older revision		Revision as of 07:08, 28 March 2018
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	<StructureSection load='5z25' size='340' side='right' caption='[[5z25]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5z25' size='340' side='right' caption='[[5z25]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z25]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z25 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z25]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquae Aquae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z25 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cycB2, aq_1550 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5z25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z25 OCA], [http://pdbe.org/5z25 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z25 RCSB], [http://www.ebi.ac.uk/pdbsum/5z25 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z25 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5z25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z25 OCA], [http://pdbe.org/5z25 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z25 RCSB], [http://www.ebi.ac.uk/pdbsum/5z25 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z25 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aquae]]
	[[Category: Higuchi, Y]]		[[Category: Higuchi, Y]]
	[[Category: Hirota, S]]		[[Category: Hirota, S]]

OCA at 05:05, 8 March 2018

OCA — Thu, 08 Mar 2018 05:05:47 GMT

←Older revision		Revision as of 05:05, 8 March 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5z25 is ~~ON HOLD until Paper~~ Publication	+	==Trimeric Alpha-Helix-Inserted Circular Permutant of Cytochrome c555==
		+	<StructureSection load='5z25' size='340' side='right' caption='[[5z25]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5z25]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z25 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5z25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z25 OCA], [http://pdbe.org/5z25 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z25 RCSB], [http://www.ebi.ac.uk/pdbsum/5z25 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z25 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Highly-ordered protein structures have gained interest for future uses for biomaterials. Herein, we constructed a building block protein (BBP) by the circular permutation of the hyperthermostable Aquifex aeolicus cytochrome (cyt) c555, and assembled BBP into a triangle-shaped trimer and a tetrahedral structure. The angle of the intermolecular interactions of BBP was controlled by cleaving the domain-swapping hinge loop of cyt c555 and connecting the original N- and C-terminal alpha-helices with an alpha-helical linker. We obtained BBP oligomers up to ~40 mers, with a relatively large amount of trimers. According to the X-ray crystallographic analysis of the BBP trimer, the N-terminal region of one BBP molecule interacted intermolecularly with the C-terminal region of another BBP molecule, resulting in a triangle-shaped structure with an edge length of 68 A. Additionally, four trimers assembled into a unique tetrahedral structure in the crystal. These results demonstrate that the circular permutation connecting the original N- and C-terminal alpha-helices with an alpha-helical linker may be useful for constructing organized protein structures.

-	~~Authors: Oda~~, A., Nagao, S., Yamanaka, M., Ueda, I., Shibata, N., Higuchi, Y., Hirota, S.	+	Construction of a Triangle-Shaped Trimer and a Tetrahedral Structure Using an alpha-Helix-Inserted Circular Permutant of Cytochrome c(5)(5)(5).,Oda A, Nagao S, Yamanaka M, Ueda I, Watanabe H, Uchihashi T, Shibata N, Higuchi Y, Hirota S Chem Asian J. 2018 Feb 26. doi: 10.1002/asia.201800252. PMID:29484831<ref>PMID:29484831</ref>

-	~~Description: Trimeric Alpha-Helix-Inserted Circular Permutant~~ of ~~Cytochrome c555~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Hirota, S]]~~	+	<div class="pdbe-citations 5z25" style="background-color:#fffaf0;"></div>
-	~~[[Category: Yamanaka, M]]~~	+	== References ==
-	~~[[Category: Shibata, N]]~~	+	<references/>
-	~~[[Category: Ueda, I]]~~	+	__TOC__
		+	</StructureSection>
	[[Category: Higuchi, Y]]		[[Category: Higuchi, Y]]
		+	[[Category: Hirota, S]]
	[[Category: Nagao, S]]		[[Category: Nagao, S]]
	[[Category: Oda, A]]		[[Category: Oda, A]]
		+	[[Category: Shibata, N]]
		+	[[Category: Ueda, I]]
		+	[[Category: Yamanaka, M]]
		+	[[Category: Electron transport]]
		+	[[Category: Permutant]]

OCA at 05:31, 17 January 2018

OCA — Wed, 17 Jan 2018 05:31:33 GMT

←Older revision		Revision as of 05:31, 17 January 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5z25 is ON HOLD	+	The entry 5z25 is ON HOLD until Paper Publication

	Authors: Oda, A., Nagao, S., Yamanaka, M., Ueda, I., Shibata, N., Higuchi, Y., Hirota, S.		Authors: Oda, A., Nagao, S., Yamanaka, M., Ueda, I., Shibata, N., Higuchi, Y., Hirota, S.
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	Description: Trimeric Alpha-Helix-Inserted Circular Permutant of Cytochrome c555		Description: Trimeric Alpha-Helix-Inserted Circular Permutant of Cytochrome c555
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Nagao, S]]
	[[Category: Hirota, S]]		[[Category: Hirota, S]]
	[[Category: Yamanaka, M]]		[[Category: Yamanaka, M]]
Line 13:		Line 12:
	[[Category: Ueda, I]]		[[Category: Ueda, I]]
	[[Category: Higuchi, Y]]		[[Category: Higuchi, Y]]
		+	[[Category: Nagao, S]]
	[[Category: Oda, A]]		[[Category: Oda, A]]

OCA: Protected "5z25" [edit=sysop:move=sysop]

OCA — Wed, 03 Jan 2018 04:53:28 GMT

Protected "5z25" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:53, 3 January 2018

OCA: New page: '''Unreleased structure''' The entry 5z25 is ON HOLD Authors: Oda, A., Nagao, S., Yamanaka, M., Ueda, I., Shibata, N., Higuchi, Y., Hirota, S. Description: Trimeric Alpha-Helix-Inserte...

OCA — Wed, 03 Jan 2018 04:53:27 GMT

New page: '''Unreleased structure''' The entry 5z25 is ON HOLD Authors: Oda, A., Nagao, S., Yamanaka, M., Ueda, I., Shibata, N., Higuchi, Y., Hirota, S. Description: Trimeric Alpha-Helix-Inserte...

New page

'''Unreleased structure'''

The entry 5z25 is ON HOLD

Authors: Oda, A., Nagao, S., Yamanaka, M., Ueda, I., Shibata, N., Higuchi, Y., Hirota, S.

Description: Trimeric Alpha-Helix-Inserted Circular Permutant of Cytochrome c555
[[Category: Unreleased Structures]]
[[Category: Nagao, S]]
[[Category: Hirota, S]]
[[Category: Yamanaka, M]]
[[Category: Shibata, N]]
[[Category: Ueda, I]]
[[Category: Higuchi, Y]]
[[Category: Oda, A]]