4jzp - Revision history

OCA at 11:32, 30 November 2022

OCA — Wed, 30 Nov 2022 11:32:32 GMT

←Older revision		Revision as of 11:32, 30 November 2022
Line 1:		Line 1:

	==Crystal structure of BAP31 vDED at acidic pH==		==Crystal structure of BAP31 vDED at acidic pH==
-	<StructureSection load='4jzp' size='340' side='right' caption='[[4jzp]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='4jzp' size='340' side='right'caption='[[4jzp]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4jzp]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JZP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4JZP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4jzp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JZP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JZP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~PG4~~:~~TETRAETHYLENE+GLYCOL~~'>~~PG4~~</scene>, <scene name='pdbligand=~~SO4~~:~~SULFATE~~+~~ION~~'>~~SO4~~</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</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=4jzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jzp OCA], [https://pdbe.org/4jzp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jzp RCSB], [https://www.ebi.ac.uk/pdbsum/4jzp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jzp ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jzl\|4jzl]]</td></tr>~~	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BCAP31, BAP31, DXS1357E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4jzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jzp OCA], [~~http~~://pdbe.org/4jzp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4jzp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4jzp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4jzp ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/BAP31_HUMAN BAP31_HUMAN]] BCAP31 is deleted in the chromosome Xq28 deletion syndrome which involves BCAP31 and the and the promoter region of ABCD1.	+	[https://www.uniprot.org/uniprot/BAP31_HUMAN BAP31_HUMAN] BCAP31 is deleted in the chromosome Xq28 deletion syndrome which involves BCAP31 and the and the promoter region of ABCD1.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BAP31_HUMAN BAP31_HUMAN]] May play a role in anterograde transport of membrane proteins from the endoplasmic reticulum to the Golgi. May be involved in CASP8-mediated apoptosis.<ref>PMID:9396746</ref> <ref>PMID:10958671</ref>	+	[https://www.uniprot.org/uniprot/BAP31_HUMAN BAP31_HUMAN] May play a role in anterograde transport of membrane proteins from the endoplasmic reticulum to the Golgi. May be involved in CASP8-mediated apoptosis.<ref>PMID:9396746</ref> <ref>PMID:10958671</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: Guettou, F]]	+	[[Category: Large Structures]]
-	[[Category: Low, C]]	+	[[Category: Guettou F]]
-	[[Category: Maddi, K]]	+	[[Category: Low C]]
-	[[Category: Moberg, P]]	+	[[Category: Maddi K]]
-	[[Category: Nordlund, P]]	+	[[Category: Moberg P]]
-	[[Category: Quistgaard~~, E M]]~~	+	[[Category: Nordlund P]]
-	~~[[Category: Apoptosis]]~~	+	[[Category: Quistgaard EM]]
-	~~[[Category: Transport protein~~]]	+

OCA at 17:54, 11 August 2016

OCA — Thu, 11 Aug 2016 17:54:56 GMT

←Older revision		Revision as of 17:54, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of BAP31 vDED at acidic pH==		==Crystal structure of BAP31 vDED at acidic pH==
	<StructureSection load='4jzp' size='340' side='right' caption='[[4jzp]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='4jzp' size='340' side='right' caption='[[4jzp]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4jzp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JZP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JZP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4jzp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JZP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JZP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jzl\|4jzl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jzl\|4jzl]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BCAP31, BAP31, DXS1357E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BCAP31, BAP31, DXS1357E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4jzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jzp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jzp RCSB], [http://www.ebi.ac.uk/pdbsum/4jzp PDBsum]</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=4jzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jzp OCA], [http://pdbe.org/4jzp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jzp RCSB], [http://www.ebi.ac.uk/pdbsum/4jzp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jzp ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 21:		Line 22:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4jzp" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Guettou, F]]		[[Category: Guettou, F]]
	[[Category: Low, C]]		[[Category: Low, C]]

OCA at 14:25, 5 January 2015

OCA — Mon, 05 Jan 2015 14:25:47 GMT

←Older revision		Revision as of 14:25, 5 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4jzp\| PDB=4jzp \| SCENE= }}~~	+	==Crystal structure of BAP31 vDED at acidic pH==
-	===Crystal structure of BAP31 vDED at acidic pH===	+	<StructureSection load='4jzp' size='340' side='right' caption='[[4jzp]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23967155}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4jzp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JZP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JZP FirstGlance]. <br>
-	==Disease==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jzl\|4jzl]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BCAP31, BAP31, DXS1357E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=4jzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jzp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jzp RCSB], [http://www.ebi.ac.uk/pdbsum/4jzp PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
	[[http://www.uniprot.org/uniprot/BAP31_HUMAN BAP31_HUMAN]] BCAP31 is deleted in the chromosome Xq28 deletion syndrome which involves BCAP31 and the and the promoter region of ABCD1.		[[http://www.uniprot.org/uniprot/BAP31_HUMAN BAP31_HUMAN]] BCAP31 is deleted in the chromosome Xq28 deletion syndrome which involves BCAP31 and the and the promoter region of ABCD1.
-		+	== Function ==
-	==Function==	+
	[[http://www.uniprot.org/uniprot/BAP31_HUMAN BAP31_HUMAN]] May play a role in anterograde transport of membrane proteins from the endoplasmic reticulum to the Golgi. May be involved in CASP8-mediated apoptosis.<ref>PMID:9396746</ref> <ref>PMID:10958671</ref>		[[http://www.uniprot.org/uniprot/BAP31_HUMAN BAP31_HUMAN]] May play a role in anterograde transport of membrane proteins from the endoplasmic reticulum to the Golgi. May be involved in CASP8-mediated apoptosis.<ref>PMID:9396746</ref> <ref>PMID:10958671</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Two members of the B-cell associated 31 (BAP31) family are found in humans; BAP29 and BAP31. These are ubiquitously expressed receptors residing in the endoplasmic reticulum. BAP31 functions in sorting of membrane proteins and in caspase-8 mediated apoptosis, while BAP29 appears to mainly corroborate with BAP31 in sorting. The N-terminal half of these proteins is membrane-bound while the C-terminal half is cytoplasmic. The latter include the so called variant of death effector domain (vDED), which shares weak sequence homology with DED domains. Here we present two structures of BAP31 vDED determined from a single and a twinned crystal, grown at pH 8.0 and pH 4.2, respectively. These structures show that BAP31 vDED forms a dimeric parallel coiled coil with no structural similarity to DED domains. Solution studies support this conclusion and strongly suggest that an additional alpha-helical domain is present in the C-terminal cytoplasmic region, probably forming a second coiled coil. The thermal stability of BAP31 vDED is quite modest at neutral pH, suggesting that it may assemble in a dynamic fashion in vivo. Surprisingly, BAP29 vDED is partially unfolded at pH 7, while a coiled coil is formed at pH 4.2 in vitro. It is however likely that folding of the domain is triggered by other factors than low pH in vivo. We found no evidence for direct interaction of the cytoplasmic domains of BAP29 and BAP31.

-	~~==About this Structure==~~	+	Structural and Biophysical Characterization of the Cytoplasmic Domains of Human BAP29 and BAP31.,Quistgaard EM, Low C, Moberg P, Guettou F, Maddi K, Nordlund P PLoS One. 2013;8(8):e71111. doi: 10.1371/journal.pone.0071111. PMID:23967155<ref>PMID:23967155</ref>
-	~~[[4jzp]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4JZP OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023967155</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Guettou, F.]]	+	[[Category: Guettou, F]]
-	[[Category: Low, C.]]	+	[[Category: Low, C]]
-	[[Category: Maddi, K.]]	+	[[Category: Maddi, K]]
-	[[Category: Moberg, P.]]	+	[[Category: Moberg, P]]
-	[[Category: Nordlund, P.]]	+	[[Category: Nordlund, P]]
-	[[Category: Quistgaard, E M.]]	+	[[Category: Quistgaard, E M]]
	[[Category: Apoptosis]]		[[Category: Apoptosis]]
	[[Category: Transport protein]]		[[Category: Transport protein]]

OCA at 08:09, 29 September 2013

OCA — Sun, 29 Sep 2013 08:09:21 GMT

←Older revision		Revision as of 08:09, 29 September 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4jzp\| PDB=4jzp \| SCENE= }}
		+	===Crystal structure of BAP31 vDED at acidic pH===
		+	{{ABSTRACT_PUBMED_23967155}}

-	~~The entry 4jzp~~ is ~~ON HOLD until Paper Publication~~	+	==Disease==
		+	[[http://www.uniprot.org/uniprot/BAP31_HUMAN BAP31_HUMAN]] BCAP31 is deleted in the chromosome Xq28 deletion syndrome which involves BCAP31 and the and the promoter region of ABCD1.

-	~~Authors~~: ~~Quistgaard, E~~.M.~~, Low, C~~.~~, Moberg, P., Guettou, F., Maddi, K., Nordlund, P~~.	+	==Function==
		+	[[http://www.uniprot.org/uniprot/BAP31_HUMAN BAP31_HUMAN]] May play a role in anterograde transport of membrane proteins from the endoplasmic reticulum to the Golgi. May be involved in CASP8-mediated apoptosis.<ref>PMID:9396746</ref> <ref>PMID:10958671</ref>

-	~~Description: Crystal~~ structure ~~of BAP31 vDED at acidic pH~~	+	==About this Structure==
		+	[[4jzp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JZP OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023967155</ref><references group="xtra"/><references/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Guettou, F.]]
		+	[[Category: Low, C.]]
		+	[[Category: Maddi, K.]]
		+	[[Category: Moberg, P.]]
		+	[[Category: Nordlund, P.]]
		+	[[Category: Quistgaard, E M.]]
		+	[[Category: Apoptosis]]
		+	[[Category: Transport protein]]

OCA: Protected "4jzp" [edit=sysop:move=sysop]

OCA — Wed, 17 Apr 2013 20:03:58 GMT

Protected "4jzp" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:03, 17 April 2013

OCA: New page: '''Unreleased structure''' The entry 4jzp is ON HOLD until Paper Publication Authors: Quistgaard, E.M., Low, C., Moberg, P., Guettou, F., Maddi, K., Nordlund, P. Description: Crystal s...

OCA — Wed, 17 Apr 2013 20:03:57 GMT

New page: '''Unreleased structure''' The entry 4jzp is ON HOLD until Paper Publication Authors: Quistgaard, E.M., Low, C., Moberg, P., Guettou, F., Maddi, K., Nordlund, P. Description: Crystal s...

New page

'''Unreleased structure'''

The entry 4jzp is ON HOLD until Paper Publication

Authors: Quistgaard, E.M., Low, C., Moberg, P., Guettou, F., Maddi, K., Nordlund, P.

Description: Crystal structure of BAP31 vDED at acidic pH