7e99 - Revision history

OCA at 16:48, 29 November 2023

2023-11-29T16:48:57Z

←Older revision		Revision as of 16:48, 29 November 2023
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-	====	+	==Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 13% oxygen saturation==
-	<StructureSection load='7e99' size='340' side='right'caption='[[7e99]]' scene=''>	+	<StructureSection load='7e99' size='340' side='right'caption='[[7e99]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7e99]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Oligobrachia_mashikoi Oligobrachia mashikoi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7E99 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E99 FirstGlance]. <br>
-	</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=7e99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e99 OCA], [https://pdbe.org/7e99 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e99 RCSB], [https://www.ebi.ac.uk/pdbsum/7e99 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e99 ProSAT]</span></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]] 2.1Å</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>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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=7e99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e99 OCA], [https://pdbe.org/7e99 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e99 RCSB], [https://www.ebi.ac.uk/pdbsum/7e99 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e99 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/GLBA1_OLIMA GLBA1_OLIMA] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cooperative oxygen binding of hemoglobin (Hb) has been studied for over half a century as a representative example of the allostericity of proteins. The most important problem remaining to be solved is the lack of structural information on the intermediates between the oxygenated and deoxygenated forms. In order to characterize the intermediate structures, it is necessary to obtain intermediate-state crystals, determine their oxygen saturations and then determine the oxygen saturations of each of their constituent subunits, all of which are challenging issues even now. Here, intermediate forms of the 400 kDa giant Hb from the tubeworm Oligobrachia mashikoi are reported. To overcome the above problems without any artificial modifications to the protein or prosthetic groups, intermediate crystals of the giant Hb were prepared from fully oxygenated crystals by a soaking method. The oxygen saturation of the crystals was measured by in situ observation with a microspectrophotometer using thin plate crystals processed by an ultraviolet laser to avoid saturation of absorption. The oxygen saturation of each subunit was determined by occupancy refinement of the bound oxygen based on ambient temperature factors. The obtained structures reveal the detailed relationship between the structural transition and oxygen dissociation. The dimer subassembly of the giant Hb shows strong correlation with the local structural changes at the heme pockets. Although some local ternary-structural changes occur in the early stages of the structural transition, the associated global ternary-structural and quaternary-structural changes might arise at about 50% oxygen saturation. The models based on coarse snapshots of the allosteric transition support the conventional two-state model of Hbs and provide the missing pieces of the intermediate structures that are required for full understanding of the allosteric nature of Hbs in detail.
		+
		+	Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state.,Numoto N, Kawano Y, Okumura H, Baba S, Fukumori Y, Miki K, Ito N IUCrJ. 2021 Sep 30;8(Pt 6):954-962. doi: 10.1107/S2052252521009386. eCollection , 2021 Nov 1. PMID:34804547<ref>PMID:34804547</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7e99" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Hemoglobin 3D structures\|Hemoglobin 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Oligobrachia mashikoi]]
		+	[[Category: Baba S]]
		+	[[Category: Fukumori Y]]
		+	[[Category: Ito N]]
		+	[[Category: Kawano Y]]
		+	[[Category: Miki K]]
		+	[[Category: Numoto N]]
		+	[[Category: Okumura H]]

OCA at 05:30, 6 October 2021

2021-10-06T05:30:20Z

←Older revision		Revision as of 05:30, 6 October 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7e99 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7e99' size='340' side='right'caption='[[7e99]]' scene=''>
-	~~Authors~~: ~~Numoto, N~~.~~, Kawano, Y~~.~~, Okumura, H~~.~~, Baba, S~~.~~, Fukumori, Y~~.~~, Miki, K~~.~~, Ito, N~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 13% oxygen saturation~~	+	</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=7e99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e99 OCA], [https://pdbe.org/7e99 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e99 RCSB], [https://www.ebi.ac.uk/pdbsum/7e99 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e99 ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Ito~~, ~~N]]~~	+	__TOC__
-	[~~[Category~~: ~~Okumura, H~~]]	+	</StructureSection>
-	[~~[Category~~: ~~Kawano~~, ~~Y]]~~	+	[[Category: Large Structures]]
-	[~~[Category~~: ~~Baba~~, ~~S]]~~	+	[[Category: Z-disk]]
-	[~~[Category~~: ~~Numoto, N]~~]	+
-	[[Category: ~~Fukumori, Y~~]]	+
-	[[Category: ~~Miki, K~~]]	+

OCA at 05:21, 24 March 2021

2021-03-24T05:21:48Z

←Older revision		Revision as of 05:21, 24 March 2021
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	Authors: Numoto, N., Kawano, Y., Okumura, H., Baba, S., Fukumori, Y., Miki, K., Ito, N.		Authors: Numoto, N., Kawano, Y., Okumura, H., Baba, S., Fukumori, Y., Miki, K., Ito, N.

-	Description: Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 69% oxygen saturation	+	Description: Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 13% oxygen saturation
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Ito, N]]		[[Category: Ito, N]]
-	[[Category: Numoto, N]]
	[[Category: Okumura, H]]		[[Category: Okumura, H]]
	[[Category: Kawano, Y]]		[[Category: Kawano, Y]]
-	[[Category: Fukumori, Y]]
	[[Category: Baba, S]]		[[Category: Baba, S]]
		+	[[Category: Numoto, N]]
		+	[[Category: Fukumori, Y]]
	[[Category: Miki, K]]		[[Category: Miki, K]]

OCA at 05:16, 17 March 2021

2021-03-17T05:16:18Z

←Older revision		Revision as of 05:16, 17 March 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7e99 is ON HOLD	+	The entry 7e99 is ON HOLD until Paper Publication

	Authors: Numoto, N., Kawano, Y., Okumura, H., Baba, S., Fukumori, Y., Miki, K., Ito, N.		Authors: Numoto, N., Kawano, Y., Okumura, H., Baba, S., Fukumori, Y., Miki, K., Ito, N.
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	Description: Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 69% oxygen saturation		Description: Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 69% oxygen saturation
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Ito, N]]
		+	[[Category: Numoto, N]]
	[[Category: Okumura, H]]		[[Category: Okumura, H]]
-	[[Category: Fukumori, Y]]
	[[Category: Kawano, Y]]		[[Category: Kawano, Y]]
		+	[[Category: Fukumori, Y]]
	[[Category: Baba, S]]		[[Category: Baba, S]]
-	[[Category: Numoto, N]]
	[[Category: Miki, K]]		[[Category: Miki, K]]
-	[[Category: Ito, N]]

OCA: Protected "7e99" [edit=sysop:move=sysop]

2021-03-10T14:35:48Z

Protected "7e99" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:35, 10 March 2021

OCA: New page: '''Unreleased structure''' The entry 7e99 is ON HOLD Authors: Numoto, N., Kawano, Y., Okumura, H., Baba, S., Fukumori, Y., Miki, K., Ito, N. Description: Oxy-deoxy intermediate of 400 ...

2021-03-10T14:35:46Z

New page: '''Unreleased structure''' The entry 7e99 is ON HOLD Authors: Numoto, N., Kawano, Y., Okumura, H., Baba, S., Fukumori, Y., Miki, K., Ito, N. Description: Oxy-deoxy intermediate of 400 ...

New page

'''Unreleased structure'''

The entry 7e99 is ON HOLD

Authors: Numoto, N., Kawano, Y., Okumura, H., Baba, S., Fukumori, Y., Miki, K., Ito, N.

Description: Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 69% oxygen saturation
[[Category: Unreleased Structures]]
[[Category: Okumura, H]]
[[Category: Fukumori, Y]]
[[Category: Kawano, Y]]
[[Category: Baba, S]]
[[Category: Numoto, N]]
[[Category: Miki, K]]
[[Category: Ito, N]]