5awi - Revision history

OCA at 15:50, 8 November 2023

2023-11-08T15:50:18Z

←Older revision		Revision as of 15:50, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5awi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AWI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AWI FirstGlance]. <br>		<table><tr><td colspan='2'>[[5awi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AWI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AWI FirstGlance]. <br>
-	</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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.85Å</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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5awi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5awi OCA], [https://pdbe.org/5awi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5awi RCSB], [https://www.ebi.ac.uk/pdbsum/5awi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5awi 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=5awi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5awi OCA], [https://pdbe.org/5awi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5awi RCSB], [https://www.ebi.ac.uk/pdbsum/5awi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5awi ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:28, 31 May 2023

2023-05-31T06:28:11Z

←Older revision		Revision as of 06:28, 31 May 2023
Line 3:		Line 3:
	<StructureSection load='5awi' size='340' side='right'caption='[[5awi]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='5awi' size='340' side='right'caption='[[5awi]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5awi]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AWI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5AWI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5awi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AWI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AWI 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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>~~	+	</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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bc5\|2bc5]]</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=5awi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5awi OCA], [https://pdbe.org/5awi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5awi RCSB], [https://www.ebi.ac.uk/pdbsum/5awi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5awi ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cybC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=5awi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5awi OCA], [~~http~~://pdbe.org/5awi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5awi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5awi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5awi ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/C562_ECOLX C562_ECOLX]] Electron-transport protein of unknown function.	+	[https://www.uniprot.org/uniprot/C562_ECOLX C562_ECOLX] Electron-transport protein of unknown function.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protein nanostructures have been gaining in interest, along with developments in new methods for construction of novel nanostructures. We have previously shown that c-type cytochromes and myoglobin form oligomers by domain swapping. Herein, we show that a four-helix bundle protein cyt cb(562), with the cyt b(562) heme attached to the protein moiety by two Cys residues insertion, forms a domain-swapped dimer. Dimeric cyt cb(562) did not dissociate to monomers at 4 degrees C, whereas dimeric cyt b(562) dissociated under the same conditions, showing that heme attachment to the protein moiety stabilizes the domain-swapped structure. According to X-ray crystallographic analysis of dimeric cyt cb(562), the two helices in the N-terminal region of one protomer interacted with the other two helices in the C-terminal region of the other protomer, where Lys51-Asp54 served as a hinge loop. The heme coordination structure of the dimer was similar to that of the monomer. In the crystal, three domain-swapped cyt cb(562) dimers formed a unique cage structure with a Zn-SO(4) cluster inside the cavity. The Zn-SO(4) cluster consisted of fifteen Zn(2+) and seven SO(4)(2-) ions, whereas six additional Zn(2+) ions were detected inside the cavity. The cage structure was stabilized by coordination of the amino acid side chains of the dimers to the Zn(2+) ions and connection of two four-helix bundle units through the conformation-adjustable hinge loop. These results show that domain swapping can be applied in the construction of unique protein nanostructures.
		+
		+	Domain-swapped cytochrome cb(562) dimer and its nanocage encapsulating a Zn-SO(4) cluster in the internal cavity.,Miyamoto T, Kuribayashi M, Nagao S, Shomura Y, Higuchi Y, Hirota S Chem Sci. 2015 Dec 1;6(12):7336-7342. doi: 10.1039/c5sc02428e. Epub 2015 Sep 22. PMID:28791095<ref>PMID:28791095</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5awi" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Cytochrome b5 3D structures\|Cytochrome b5 3D structures]]		*[[Cytochrome b5 3D structures\|Cytochrome b5 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Higuchi, Y]]	+	[[Category: Higuchi Y]]
-	[[Category: Hirota, S]]	+	[[Category: Hirota S]]
-	[[Category: Kuribayashi, M]]	+	[[Category: Kuribayashi M]]
-	[[Category: Miyamoto, T]]	+	[[Category: Miyamoto T]]
-	[[Category: Nagao, S]]	+	[[Category: Nagao S]]
-	[[Category: Shomura, Y]]	+	[[Category: Shomura Y]]
-	~~[[Category: Electron transport~~]]	+

OCA at 10:48, 2 October 2019

2019-10-02T10:48:48Z

←Older revision		Revision as of 10:48, 2 October 2019
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5awi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AWI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AWI FirstGlance]. <br>		<table><tr><td colspan='2'>[[5awi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AWI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AWI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~HEM~~:~~PROTOPORPHYRIN~~+~~IX+CONTAINING+FE~~'>~~HEM~~</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bc5\|2bc5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bc5\|2bc5]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cybC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cybC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>

OCA at 07:24, 3 July 2019

2019-07-03T07:24:51Z

←Older revision		Revision as of 07:24, 3 July 2019
Line 1:		Line 1:
		+
	==Domain-swapped cytochrome cb562 dimer==		==Domain-swapped cytochrome cb562 dimer==
-	<StructureSection load='5awi' size='340' side='right' caption='[[5awi]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='5awi' size='340' side='right'caption='[[5awi]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5awi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AWI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AWI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5awi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AWI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AWI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bc5\|2bc5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bc5\|2bc5]]</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=5awi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5awi OCA], [http://pdbe.org/5awi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5awi RCSB], [http://www.ebi.ac.uk/pdbsum/5awi PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cybC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=5awi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5awi OCA], [http://pdbe.org/5awi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5awi RCSB], [http://www.ebi.ac.uk/pdbsum/5awi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5awi ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/C562_ECOLX C562_ECOLX]] Electron-transport protein of unknown function.		[[http://www.uniprot.org/uniprot/C562_ECOLX C562_ECOLX]] Electron-transport protein of unknown function.
		+
		+	==See Also==
		+	*[[Cytochrome b5 3D structures\|Cytochrome b5 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Higuchi, Y]]		[[Category: Higuchi, Y]]
	[[Category: Hirota, S]]		[[Category: Hirota, S]]

OCA at 05:32, 22 October 2015

2015-10-22T05:32:58Z

←Older revision		Revision as of 05:32, 22 October 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Domain-swapped cytochrome cb562 dimer==
-		+	<StructureSection load='5awi' size='340' side='right' caption='[[5awi]], [[Resolution\|resolution]] 1.85Å' scene=''>
-	~~The entry~~ 5awi is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5awi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AWI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AWI FirstGlance]. <br>
-	~~Authors~~: ~~Miyamoto, T~~.~~, Kuribayashi, M~~.~~, Nagao, S~~.~~, Shomura, Y~~.~~, Higuchi, Y~~.~~, Hirota, S~~.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bc5\|2bc5]]</td></tr>
-	~~Description~~: ~~Domain-swapped cytochrome cb562 dimer~~	+	<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=5awi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5awi OCA], [http://pdbe.org/5awi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5awi RCSB], [http://www.ebi.ac.uk/pdbsum/5awi PDBsum]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Miyamoto~~, T]]	+	== Function ==
-	[[~~Category~~: ~~Hirota, S~~]]	+	[[http://www.uniprot.org/uniprot/C562_ECOLX C562_ECOLX]] Electron-transport protein of unknown function.
		+	__TOC__
		+	</StructureSection>
	[[Category: Higuchi, Y]]		[[Category: Higuchi, Y]]
		+	[[Category: Hirota, S]]
		+	[[Category: Kuribayashi, M]]
		+	[[Category: Miyamoto, T]]
	[[Category: Nagao, S]]		[[Category: Nagao, S]]
	[[Category: Shomura, Y]]		[[Category: Shomura, Y]]
-	[[Category: ~~Kuribayashi, M~~]]	+	[[Category: Electron transport]]

OCA at 12:19, 22 July 2015

2015-07-22T12:19:24Z

←Older revision		Revision as of 12:19, 22 July 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Miyamoto, T., Kuribayashi, M., Nagao, S., Shomura, Y., Higuchi, Y., Hirota, S.		Authors: Miyamoto, T., Kuribayashi, M., Nagao, S., Shomura, Y., Higuchi, Y., Hirota, S.

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

2015-07-15T11:43:18Z

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

←Older revision

Revision as of 11:43, 15 July 2015

OCA: New page: '''Unreleased structure''' The entry 5awi is ON HOLD Authors: Miyamoto, T., Kuribayashi, M., Nagao, S., Shomura, Y., Higuchi, Y., Hirota, S. Description: Domain-swapped cytochrome cb56...

2015-07-15T11:43:17Z

New page: '''Unreleased structure''' The entry 5awi is ON HOLD Authors: Miyamoto, T., Kuribayashi, M., Nagao, S., Shomura, Y., Higuchi, Y., Hirota, S. Description: Domain-swapped cytochrome cb56...

New page

'''Unreleased structure'''

The entry 5awi is ON HOLD

Authors: Miyamoto, T., Kuribayashi, M., Nagao, S., Shomura, Y., Higuchi, Y., Hirota, S.

Description: Domain-swapped cytochrome cb562 dimer
[[Category: Unreleased Structures]]
[[Category: Miyamoto, T]]
[[Category: Hirota, S]]
[[Category: Higuchi, Y]]
[[Category: Nagao, S]]
[[Category: Shomura, Y]]
[[Category: Kuribayashi, M]]