5ktg - Revision history

OCA at 10:54, 27 September 2023

OCA — Wed, 27 Sep 2023 10:54:02 GMT

←Older revision		Revision as of 10:54, 27 September 2023
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	<StructureSection load='5ktg' size='340' side='right'caption='[[5ktg]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5ktg' size='340' side='right'caption='[[5ktg]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ktg]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aeqvi Aeqvi~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KTG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KTG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ktg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KTG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KTG FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non~~-~~Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CR2:{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CR2</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]] 2.802Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bak1, Bak ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6100 AEQVI])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CR2:{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CR2</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=5ktg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ktg OCA], [~~http~~://pdbe.org/5ktg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ktg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ktg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ktg 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=5ktg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ktg OCA], [https://pdbe.org/5ktg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ktg RCSB], [https://www.ebi.ac.uk/pdbsum/5ktg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ktg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI]] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.	+	[https://www.uniprot.org/uniprot/BAK_MOUSE BAK_MOUSE] In the presence of an appropriate stimulus, accelerates programmed cell death by binding to, and antagonizing the anti-apoptotic action of BCL2 (By similarity).[https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
	<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: ~~Aeqvi~~]]	+	[[Category: Aequorea victoria]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Choe, J Y~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Mandal, T]]~~	+	[[Category: Choe J-Y]]
-	~~[[Category: Oh, K~~ J]]	+	[[Category: Mandal T]]
-	~~[[Category: Apoptosis]]~~	+	[[Category: Oh KJ]]
-	~~[[Category: Apoptosis regulator]]~~	+
-	~~[[Category: Bcl~~-~~2 family protein~~]]	+
-	[[Category: ~~Mitochondrial outer membrane permeabilization~~]]	+
-	[[Category: ~~Pore-forming protein~~]]	+

OCA at 12:21, 25 December 2019

OCA — Wed, 25 Dec 2019 12:21:10 GMT

←Older revision		Revision as of 12:21, 25 December 2019
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	==Crystal structure of mouse Bak BH3-in-groove homodimer (GFP)==		==Crystal structure of mouse Bak BH3-in-groove homodimer (GFP)==
-	<StructureSection load='5ktg' size='340' side='right' caption='[[5ktg]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='5ktg' size='340' side='right'caption='[[5ktg]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ktg]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KTG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KTG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ktg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeqvi Aeqvi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KTG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KTG FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CR2:{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CR2</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CR2:{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CR2</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bak1, Bak ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6100 AEQVI])</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=5ktg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ktg OCA], [http://pdbe.org/5ktg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ktg RCSB], [http://www.ebi.ac.uk/pdbsum/5ktg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ktg 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=5ktg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ktg OCA], [http://pdbe.org/5ktg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ktg RCSB], [http://www.ebi.ac.uk/pdbsum/5ktg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ktg ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 5ktg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ktg" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Green Fluorescent Protein 3D structures\|Green Fluorescent Protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aeqvi]]
		+	[[Category: Large Structures]]
	[[Category: Choe, J Y]]		[[Category: Choe, J Y]]
	[[Category: Mandal, T]]		[[Category: Mandal, T]]

OCA at 00:07, 10 September 2016

OCA — Sat, 10 Sep 2016 00:07:33 GMT

←Older revision		Revision as of 00:07, 10 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ktg is ~~ON HOLD~~	+	==Crystal structure of mouse Bak BH3-in-groove homodimer (GFP)==
		+	<StructureSection load='5ktg' size='340' side='right' caption='[[5ktg]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ktg]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KTG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KTG FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CR2:{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CR2</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=5ktg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ktg OCA], [http://pdbe.org/5ktg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ktg RCSB], [http://www.ebi.ac.uk/pdbsum/5ktg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ktg ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI]] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In mitochondrial apoptosis, Bak is activated by death signals to form pores of unknown structure on the mitochondrial outer membrane via homooligomerization. Cytochrome c and other apoptotic factors are released from the intermembrane space through these pores, initiating downstream apoptosis events. Using chemical crosslinking and double electron electron resonance (DEER)-derived distance measurements between specific structural elements in Bak, here we clarify how the Bak pore is assembled. We propose that previously described BH3-in-groove homodimers (BGH) are juxtaposed via the 'alpha3/alpha5' interface, in which the C-termini of helices alpha3 and alpha5 are in close proximity between two neighboring Bak homodimers. This interface is observed concomitantly with the well-known 'alpha6:alpha6' interface. We also mapped the contacts between Bak homodimers and the lipid bilayer based on EPR spectroscopy topology studies. Our results suggest a model for the lipidic Bak pore, whereby the mitochondrial targeting C-terminal helix does not change topology to accommodate the lining of the pore lumen by BGH.

-	~~Authors: Mandal~~, T., Choe, ~~J.-Y.~~, Oh, K.J.	+	Assembly of Bak homodimers into higher order homooligomers in the mitochondrial apoptotic pore.,Mandal T, Shin S, Aluvila S, Chen HC, Grieve C, Choe JY, Cheng EH, Hustedt EJ, Oh KJ Sci Rep. 2016 Aug 4;6:30763. doi: 10.1038/srep30763. PMID:27488021<ref>PMID:27488021</ref>

-	~~Description: Crystal structure~~ of ~~mouse Bak BH3~~-in-~~groove homodimer (GFP)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Oh, K.J]]~~	+	<div class="pdbe-citations 5ktg" style="background-color:#fffaf0;"></div>
-	[[Category: Choe, J.-Y]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Choe, J Y]]
	[[Category: Mandal, T]]		[[Category: Mandal, T]]
		+	[[Category: Oh, K J]]
		+	[[Category: Apoptosis]]
		+	[[Category: Apoptosis regulator]]
		+	[[Category: Bcl-2 family protein]]
		+	[[Category: Mitochondrial outer membrane permeabilization]]
		+	[[Category: Pore-forming protein]]

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

OCA — Tue, 26 Jul 2016 12:52:43 GMT

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

←Older revision

Revision as of 12:52, 26 July 2016

OCA: New page: '''Unreleased structure''' The entry 5ktg is ON HOLD Authors: Mandal, T., Choe, J.-Y., Oh, K.J. Description: Crystal structure of mouse Bak BH3-in-groove homodimer (GFP) [[Category: Un...

OCA — Tue, 26 Jul 2016 12:52:41 GMT

New page: '''Unreleased structure''' The entry 5ktg is ON HOLD Authors: Mandal, T., Choe, J.-Y., Oh, K.J. Description: Crystal structure of mouse Bak BH3-in-groove homodimer (GFP) [[Category: Un...

New page

'''Unreleased structure'''

The entry 5ktg is ON HOLD

Authors: Mandal, T., Choe, J.-Y., Oh, K.J.

Description: Crystal structure of mouse Bak BH3-in-groove homodimer (GFP)
[[Category: Unreleased Structures]]
[[Category: Oh, K.J]]
[[Category: Choe, J.-Y]]
[[Category: Mandal, T]]