6i3t - Revision history

OCA at 11:45, 24 January 2024

OCA — Wed, 24 Jan 2024 11:45:48 GMT

←Older revision		Revision as of 11:45, 24 January 2024
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	<StructureSection load='6i3t' size='340' side='right'caption='[[6i3t]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6i3t' size='340' side='right'caption='[[6i3t]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6i3t]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I3T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6I3T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6i3t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I3T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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]] 2Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ngb ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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=6i3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i3t OCA], [~~http~~://pdbe.org/6i3t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6i3t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6i3t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6i3t 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=6i3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i3t OCA], [https://pdbe.org/6i3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i3t RCSB], [https://www.ebi.ac.uk/pdbsum/6i3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i3t ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NGB_MOUSE NGB_MOUSE]] Involved in oxygen transport in the brain. Hexacoordinate globin, displaying competitive binding of oxygen or the distal His residue to the iron atom. Not capable of penetrating cell membranes. The deoxygenated form exhibits nitrite reductase activity inhibiting cellular respiration via NO-binding to cytochrome c oxidase. Involved in neuroprotection during oxidative stress. May exert its anti-apoptotic activity by acting to reset the trigger level of mitochondrial cytochrome c release necessary to commit the cells to apoptosis.<ref>PMID:11473111</ref> <ref>PMID:11473128</ref>	+	[https://www.uniprot.org/uniprot/NGB_MOUSE NGB_MOUSE] Involved in oxygen transport in the brain. Hexacoordinate globin, displaying competitive binding of oxygen or the distal His residue to the iron atom. Not capable of penetrating cell membranes. The deoxygenated form exhibits nitrite reductase activity inhibiting cellular respiration via NO-binding to cytochrome c oxidase. Involved in neuroprotection during oxidative stress. May exert its anti-apoptotic activity by acting to reset the trigger level of mitochondrial cytochrome c release necessary to commit the cells to apoptosis.<ref>PMID:11473111</ref> <ref>PMID:11473128</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6i3t" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6i3t" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Neuroglobin\|Neuroglobin]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Ardiccioni, C]]	+	[[Category: Ardiccioni C]]
-	[[Category: Exertier, C]]	+	[[Category: Exertier C]]
-	[[Category: Montemiglio~~, L C~~]]	+	[[Category: Montemiglio LC]]
-	[[Category: Savino, C]]	+	[[Category: Savino C]]
-	~~[[Category: Carbon monoxide]]~~	+
-	~~[[Category: Oxygen transport]]~~	+
-	~~[[Category: Oxygen transport/storage]]~~	+
-	~~[[Category: Photodissociation~~]]	+

OCA at 06:06, 10 October 2019

OCA — Thu, 10 Oct 2019 06:06:16 GMT

←Older revision		Revision as of 06:06, 10 October 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6i3t is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of murine neuroglobin bound to CO at 40 K.==
		+	<StructureSection load='6i3t' size='340' side='right'caption='[[6i3t]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6i3t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I3T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I3T FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ngb ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=6i3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i3t OCA], [http://pdbe.org/6i3t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i3t RCSB], [http://www.ebi.ac.uk/pdbsum/6i3t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i3t ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NGB_MOUSE NGB_MOUSE]] Involved in oxygen transport in the brain. Hexacoordinate globin, displaying competitive binding of oxygen or the distal His residue to the iron atom. Not capable of penetrating cell membranes. The deoxygenated form exhibits nitrite reductase activity inhibiting cellular respiration via NO-binding to cytochrome c oxidase. Involved in neuroprotection during oxidative stress. May exert its anti-apoptotic activity by acting to reset the trigger level of mitochondrial cytochrome c release necessary to commit the cells to apoptosis.<ref>PMID:11473111</ref> <ref>PMID:11473128</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A combined biophysical approach was applied to map gas-docking sites within murine neuroglobin (Ngb), revealing snapshots of events that might govern activity and dynamics in this unique hexacoordinate globin, which is most likely to be involved in gas-sensing in the central nervous system and for which a precise mechanism of action remains to be elucidated. The application of UV-visible microspectroscopy in crystallo, solution X-ray absorption near-edge spectroscopy and X-ray diffraction experiments at 15-40 K provided the structural characterization of an Ngb photolytic intermediate by cryo-trapping and allowed direct observation of the relocation of carbon monoxide within the distal heme pocket after photodissociation. Moreover, X-ray diffraction at 100 K under a high pressure of dioxygen, a physiological ligand of Ngb, unravelled the existence of a storage site for O2 in Ngb which coincides with Xe-III, a previously described docking site for xenon or krypton. Notably, no other secondary sites were observed under our experimental conditions.

-	~~Authors: Savino~~, C., Montemiglio, L.C., ~~Ardiccioni~~, C., ~~Exertier~~, C.	+	Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments.,Ardiccioni C, Arcovito A, Della Longa S, van der Linden P, Bourgeois D, Weik M, Montemiglio LC, Savino C, Avella G, Exertier C, Carpentier P, Prange T, Brunori M, Colloc'h N, Vallone B IUCrJ. 2019 Jul 10;6(Pt 5):832-842. doi: 10.1107/S2052252519008157. eCollection, 2019 Sep 1. PMID:31576217<ref>PMID:31576217</ref>

-	~~Description: Crystal structure~~ of ~~murine neuroglobin bound to CO at 40 K~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Montemiglio, L.C~~]]	+	<div class="pdbe-citations 6i3t" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Savino, C~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Ardiccioni, C]]		[[Category: Ardiccioni, C]]
	[[Category: Exertier, C]]		[[Category: Exertier, C]]
		+	[[Category: Montemiglio, L C]]
		+	[[Category: Savino, C]]
		+	[[Category: Carbon monoxide]]
		+	[[Category: Oxygen transport]]
		+	[[Category: Oxygen transport/storage]]
		+	[[Category: Photodissociation]]

OCA at 18:31, 2 December 2018

OCA — Sun, 02 Dec 2018 18:31:21 GMT

←Older revision		Revision as of 18:31, 2 December 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6i3t is ON HOLD	+	The entry 6i3t is ON HOLD until Paper Publication

	Authors: Savino, C., Montemiglio, L.C., Ardiccioni, C., Exertier, C.		Authors: Savino, C., Montemiglio, L.C., Ardiccioni, C., Exertier, C.

-	Description: Crystal structure of murine neuroglobin bound to CO at ~~40K without illumination~~	+	Description: Crystal structure of murine neuroglobin bound to CO at 40 K.
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Montemiglio, L.C]]		[[Category: Montemiglio, L.C]]

OCA: Protected "6i3t" [edit=sysop:move=sysop]

OCA — Wed, 14 Nov 2018 06:22:07 GMT

Protected "6i3t" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:22, 14 November 2018

OCA: New page: '''Unreleased structure''' The entry 6i3t is ON HOLD Authors: Savino, C., Montemiglio, L.C., Ardiccioni, C., Exertier, C. Description: Crystal structure of murine neuroglobin bound to ...

OCA — Wed, 14 Nov 2018 06:22:05 GMT

New page: '''Unreleased structure''' The entry 6i3t is ON HOLD Authors: Savino, C., Montemiglio, L.C., Ardiccioni, C., Exertier, C. Description: Crystal structure of murine neuroglobin bound to ...

New page

'''Unreleased structure'''

The entry 6i3t is ON HOLD

Authors: Savino, C., Montemiglio, L.C., Ardiccioni, C., Exertier, C.

Description: Crystal structure of murine neuroglobin bound to CO at 40K without illumination
[[Category: Unreleased Structures]]
[[Category: Montemiglio, L.C]]
[[Category: Savino, C]]
[[Category: Ardiccioni, C]]
[[Category: Exertier, C]]