5yzf - Revision history

OCA at 08:41, 22 November 2023

OCA — Wed, 22 Nov 2023 08:41:42 GMT

←Older revision		Revision as of 08:41, 22 November 2023
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	<StructureSection load='5yzf' size='340' side='right'caption='[[5yzf]], [[Resolution\|resolution]] 1.77Å' scene=''>		<StructureSection load='5yzf' size='340' side='right'caption='[[5yzf]], [[Resolution\|resolution]] 1.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yzf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YZF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yzf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YZF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.77Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5yzf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzf OCA], [~~http~~://pdbe.org/5yzf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yzf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yzf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzf ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=5yzf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzf OCA], [https://pdbe.org/5yzf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yzf RCSB], [https://www.ebi.ac.uk/pdbsum/5yzf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~MYG_PHYCD MYG_PHYCD]~~] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.	+	[https://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Yuan, H~~]]	+	[[Category: Physeter catodon]]
-	[[Category: ~~Myoglobin]]~~	+	[[Category: Yuan H]]
-	~~[[Category: Oxygen transport~~]]	+

OCA at 09:32, 21 October 2020

OCA — Wed, 21 Oct 2020 09:32:03 GMT

←Older revision		Revision as of 09:32, 21 October 2020
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	==X-ray crystal structure of met K42C sperm whale myoglobin==		==X-ray crystal structure of met K42C sperm whale myoglobin==
-	<StructureSection load='5yzf' size='340' side='right' caption='[[5yzf]], [[Resolution\|resolution]] 1.77Å' scene=''>	+	<StructureSection load='5yzf' size='340' side='right'caption='[[5yzf]], [[Resolution\|resolution]] 1.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yzf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZF OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YZF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yzf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YZF 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></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=5yzf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzf OCA], [http://pdbe.org/5yzf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yzf RCSB], [http://www.ebi.ac.uk/pdbsum/5yzf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzf ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5yzf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzf OCA], [http://pdbe.org/5yzf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yzf RCSB], [http://www.ebi.ac.uk/pdbsum/5yzf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5yzf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5yzf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Myoglobin 3D structures\|Myoglobin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Yuan, H]]		[[Category: Yuan, H]]
	[[Category: Myoglobin]]		[[Category: Myoglobin]]
	[[Category: Oxygen transport]]		[[Category: Oxygen transport]]

OCA at 05:05, 8 March 2018

OCA — Thu, 08 Mar 2018 05:05:43 GMT

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

-	~~The entry~~ 5yzf is ~~ON HOLD until Paper~~ Publication	+	==X-ray crystal structure of met K42C sperm whale myoglobin==
		+	<StructureSection load='5yzf' size='340' side='right' caption='[[5yzf]], [[Resolution\|resolution]] 1.77Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yzf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YZF 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></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=5yzf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzf OCA], [http://pdbe.org/5yzf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yzf RCSB], [http://www.ebi.ac.uk/pdbsum/5yzf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzf ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MYG_PHYCD MYG_PHYCD]] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The structure and function of heme proteins are regulated by diverse post-translational modifications including heme-protein cross-links, with the underlying mechanisms not well understood. In this study, we introduced a Cys (K42C) close to the heme 4-vinyl group in sperm whale myoglobin (Mb) and solved its X-ray crystal structure. Interestingly, we found that K42C Mb can partially form a Cys-heme cross-link (termed K42C Mb-X) under dithiothreitol-induced reductive conditions in presence of O2, as suggested by guanidine hydrochloride-induced unfolding and heme extraction studies. Mass spectrometry (MS) studies, together with trypsin digestion studies, further indicated that a thioether bond is formed between Cys42 and the heme 4-vinyl group with an additional mass of 16Da, likely due to hydroxylation of the alphacarbon. We then proposed a plausible mechanism for the formation of the novel Cys-heme cross-link based on MS, kinetic UV-vis and electron paramagnetic resonance (EPR) studies. Moreover, the Cys-heme cross-link was shown to fine-tune the protein reactivity toward activation of H2O2. This study provides valuable insights into the post-translational modification of heme proteins, and also suggests that the Cys-heme cross-link can be induced to form in vitro, making it useful for design of new heme proteins with a non-dissociable heme and improved functions.

-	~~Authors: Yuan~~, H.	+	Formation of Cys-heme cross-link in K42C myoglobin under reductive conditions with molecular oxygen.,Cheng HM, Yuan H, Wang XJ, Xu JK, Gao SQ, Wen GB, Tan X, Lin YW J Inorg Biochem. 2018 Feb 19;182:141-149. doi: 10.1016/j.jinorgbio.2018.02.011. PMID:29477977<ref>PMID:29477977</ref>

-	~~Description: X-ray crystal structure~~ of ~~met K42C sperm whale myoglobin~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5yzf" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Yuan, H]]		[[Category: Yuan, H]]
		+	[[Category: Myoglobin]]
		+	[[Category: Oxygen transport]]

OCA at 07:03, 10 January 2018

OCA — Wed, 10 Jan 2018 07:03:55 GMT

←Older revision		Revision as of 07:03, 10 January 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Yuan, H.		Authors: Yuan, H.

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

OCA — Wed, 20 Dec 2017 04:53:39 GMT

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

←Older revision

Revision as of 04:53, 20 December 2017

OCA: New page: '''Unreleased structure''' The entry 5yzf is ON HOLD Authors: Yuan, H. Description: X-ray crystal structure of met K42C sperm whale myoglobin Category: Unreleased Structures [[Cate...

OCA — Wed, 20 Dec 2017 04:53:38 GMT

New page: '''Unreleased structure''' The entry 5yzf is ON HOLD Authors: Yuan, H. Description: X-ray crystal structure of met K42C sperm whale myoglobin Category: Unreleased Structures [[Cate...

New page

'''Unreleased structure'''

The entry 5yzf is ON HOLD

Authors: Yuan, H.

Description: X-ray crystal structure of met K42C sperm whale myoglobin
[[Category: Unreleased Structures]]
[[Category: Yuan, H]]