3u3q - Revision history

OCA at 05:56, 13 July 2022

OCA — Wed, 13 Jul 2022 05:56:27 GMT

←Older revision		Revision as of 05:56, 13 July 2022
Line 1:		Line 1:

	==The S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6)==		==The S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6)==
-	<StructureSection load='3u3q' size='340' side='right' caption='[[3u3q]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='3u3q' size='340' side='right'caption='[[3u3q]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3u3q]] is a 1 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=3U3Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3U3Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3u3q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U3Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U3Q FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3u3p\|3u3p]], [[3u3s\|3u3s]], [[3u3t\|3u3t]], [[3u3v\|3u3v]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3u3p\|3u3p]], [[3u3s\|3u3s]], [[3u3t\|3u3t]], [[3u3v\|3u3v]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TNFRSF21, DR6, UNQ437/PRO868 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TNFRSF21, DR6, UNQ437/PRO868 ([https://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=3u3q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u3q OCA], [~~http~~://pdbe.org/3u3q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3u3q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3u3q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3u3q 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=3u3q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u3q OCA], [https://pdbe.org/3u3q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u3q RCSB], [https://www.ebi.ac.uk/pdbsum/3u3q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u3q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/TNR21_HUMAN TNR21_HUMAN]] May activate NF-kappa-B and promote apoptosis. May activate JNK and be involved in T-cell differentiation. Required for both normal cell body death and axonal pruning. Trophic-factor deprivation triggers the cleavage of surface APP by beta-secretase to release sAPP-beta which is further cleaved to release an N-terminal fragment of APP (N-APP). N-APP binds TNFRSF21 triggering caspase activation and degeneration of both neuronal cell bodies (via caspase-3) and axons (via caspase-6).	+	[[https://www.uniprot.org/uniprot/TNR21_HUMAN TNR21_HUMAN]] May activate NF-kappa-B and promote apoptosis. May activate JNK and be involved in T-cell differentiation. Required for both normal cell body death and axonal pruning. Trophic-factor deprivation triggers the cleavage of surface APP by beta-secretase to release sAPP-beta which is further cleaved to release an N-terminal fragment of APP (N-APP). N-APP binds TNFRSF21 triggering caspase activation and degeneration of both neuronal cell bodies (via caspase-3) and axons (via caspase-6).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:

	==See Also==		==See Also==
-	*[[Tumor necrosis factor receptor\|Tumor necrosis factor receptor]]	+	*[[Tumor necrosis factor receptor 3D structures\|Tumor necrosis factor receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Ding, W]]		[[Category: Ding, W]]
	[[Category: Hung, L W]]		[[Category: Hung, L W]]

OCA at 20:23, 4 August 2016

OCA — Thu, 04 Aug 2016 20:23:35 GMT

←Older revision		Revision as of 20:23, 4 August 2016
Line 1:		Line 1:
		+
	==The S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6)==		==The S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6)==
	<StructureSection load='3u3q' size='340' side='right' caption='[[3u3q]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3u3q' size='340' side='right' caption='[[3u3q]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3u3q]] is a 1 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=3U3Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3U3Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3u3q]] is a 1 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=3U3Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3U3Q FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3u3p\|3u3p]], [[3u3s\|3u3s]], [[3u3t\|3u3t]], [[3u3v\|3u3v]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3u3p\|3u3p]], [[3u3s\|3u3s]], [[3u3t\|3u3t]], [[3u3v\|3u3v]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TNFRSF21, DR6, UNQ437/PRO868 ([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">TNFRSF21, DR6, UNQ437/PRO868 ([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=3u3q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u3q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3u3q RCSB], [http://www.ebi.ac.uk/pdbsum/3u3q 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=3u3q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u3q OCA], [http://pdbe.org/3u3q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3u3q RCSB], [http://www.ebi.ac.uk/pdbsum/3u3q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3u3q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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 3u3q" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 24:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Ding, W]]		[[Category: Ding, W]]
	[[Category: Hung, L W]]		[[Category: Hung, L W]]

OCA at 19:17, 24 December 2014

OCA — Wed, 24 Dec 2014 19:17:48 GMT

←Older revision		Revision as of 19:17, 24 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3u3q\| PDB=3u3q \| SCENE= }}~~	+	==The S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6)==
-	===The S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6)===	+	<StructureSection load='3u3q' size='340' side='right' caption='[[3u3q]], [[Resolution\|resolution]] 2.70Å' scene=''>
-	~~{{ABSTRACT_PUBMED_22525750}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[3u3q]] is a 1 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=3U3Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3U3Q FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3u3p\|3u3p]], [[3u3s\|3u3s]], [[3u3t\|3u3t]], [[3u3v\|3u3v]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TNFRSF21, DR6, UNQ437/PRO868 ([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=3u3q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u3q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3u3q RCSB], [http://www.ebi.ac.uk/pdbsum/3u3q PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/TNR21_HUMAN TNR21_HUMAN]] May activate NF-kappa-B and promote apoptosis. May activate JNK and be involved in T-cell differentiation. Required for both normal cell body death and axonal pruning. Trophic-factor deprivation triggers the cleavage of surface APP by beta-secretase to release sAPP-beta which is further cleaved to release an N-terminal fragment of APP (N-APP). N-APP binds TNFRSF21 triggering caspase activation and degeneration of both neuronal cell bodies (via caspase-3) and axons (via caspase-6).		[[http://www.uniprot.org/uniprot/TNR21_HUMAN TNR21_HUMAN]] May activate NF-kappa-B and promote apoptosis. May activate JNK and be involved in T-cell differentiation. Required for both normal cell body death and axonal pruning. Trophic-factor deprivation triggers the cleavage of surface APP by beta-secretase to release sAPP-beta which is further cleaved to release an N-terminal fragment of APP (N-APP). N-APP binds TNFRSF21 triggering caspase activation and degeneration of both neuronal cell bodies (via caspase-3) and axons (via caspase-6).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A subset of tumour necrosis factor receptor (TNFR) superfamily members contain death domains in their cytoplasmic tails. Death receptor 6 (DR6) is one such member and can trigger apoptosis upon the binding of a ligand by its cysteine-rich domains (CRDs). The crystal structure of the ectodomain (amino acids 1-348) of human death receptor 6 (DR6) encompassing the CRD region was phased using the anomalous signal from S atoms. In order to explore the feasibility of S-SAD phasing at longer wavelengths (beyond 2.5 A), a comparative study was performed on data collected at wavelengths of 2.0 and 2.7 A. In spite of sub-optimal experimental conditions, the 2.7 A wavelength used for data collection showed potential for S-SAD phasing. The results showed that the R(ano)/R(p.i.m.) ratio is a good indicator for monitoring the anomalous data quality when the anomalous signal is relatively strong, while d''/sig(d'') calculated by SHELXC is a more sensitive and stable indicator applicable for grading a wider range of anomalous data qualities. The use of the `parameter-space screening method' for S-SAD phasing resulted in solutions for data sets that failed during manual attempts. SAXS measurements on the ectodomain suggested that a dimer defines the minimal physical unit of an unliganded DR6 molecule in solution.
		+
		+	S-SAD phasing study of death receptor 6 and its solution conformation revealed by SAXS.,Ru H, Zhao L, Ding W, Jiao L, Shaw N, Liang W, Zhang L, Hung LW, Matsugaki N, Wakatsuki S, Liu ZJ Acta Crystallogr D Biol Crystallogr. 2012 May;68(Pt 5):521-30. Epub 2012 Apr 17. PMID:22525750<ref>PMID:22525750</ref>

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3u3q]] is~~ a ~~1 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=3U3Q OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:022525750</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Tumor necrosis factor receptor\|Tumor necrosis factor receptor]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Ding, W.]]	+	[[Category: Ding, W]]
-	[[Category: Hung, L W.]]	+	[[Category: Hung, L W]]
-	[[Category: Jiao, L Y.]]	+	[[Category: Jiao, L Y]]
-	[[Category: Liu, Z J.]]	+	[[Category: Liu, Z J]]
-	[[Category: Matsugaki, N.]]	+	[[Category: Matsugaki, N]]
-	[[Category: Ru, H.]]	+	[[Category: Ru, H]]
-	[[Category: Shaw, N.]]	+	[[Category: Shaw, N]]
-	[[Category: Wakatsuki, S.]]	+	[[Category: Wakatsuki, S]]
-	[[Category: Zhang, L G.]]	+	[[Category: Zhang, L G]]
-	[[Category: Zhao, L X.]]	+	[[Category: Zhao, L X]]
	[[Category: Apoptosis]]		[[Category: Apoptosis]]
	[[Category: Trigger apoptosis]]		[[Category: Trigger apoptosis]]

OCA at 14:28, 10 July 2013

OCA — Wed, 10 Jul 2013 14:28:31 GMT

←Older revision		Revision as of 14:28, 10 July 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_3u3q\| PDB=3u3q \| SCENE= }}
		+	===The S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6)===
		+	{{ABSTRACT_PUBMED_22525750}}

-	~~The entry 3u3q~~ is ~~ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/TNR21_HUMAN TNR21_HUMAN]] May activate NF-kappa-B and promote apoptosis. May activate JNK and be involved in T-cell differentiation. Required for both normal cell body death and axonal pruning. Trophic-factor deprivation triggers the cleavage of surface APP by beta-secretase to release sAPP-beta which is further cleaved to release an N-terminal fragment of APP (N-APP). N-APP binds TNFRSF21 triggering caspase activation and degeneration of both neuronal cell bodies (via caspase-3) and axons (via caspase-6).

-	~~Authors~~: ~~Ru, H~~.~~, Zhao, L~~.X.~~, Ding, W., Jiao, L.Y., Shaw, N., Zhang, L.G., Hung, L.W., Matsugaki, N~~.~~, Wakatsuki, S~~.~~, Liu, Z~~.J.	+	==About this Structure==
		+	[[3u3q]] is a 1 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=3U3Q OCA].

-	~~Description~~: ~~The~~ S~~-SAD phased crystal structure of Death Receptor 6 (DR6) and its solution conformation revealed by SAXS~~	+	==Reference==
		+	<ref group="xtra">PMID:022525750</ref><references group="xtra"/><references/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Ding, W.]]
		+	[[Category: Hung, L W.]]
		+	[[Category: Jiao, L Y.]]
		+	[[Category: Liu, Z J.]]
		+	[[Category: Matsugaki, N.]]
		+	[[Category: Ru, H.]]
		+	[[Category: Shaw, N.]]
		+	[[Category: Wakatsuki, S.]]
		+	[[Category: Zhang, L G.]]
		+	[[Category: Zhao, L X.]]
		+	[[Category: Apoptosis]]
		+	[[Category: Trigger apoptosis]]

OCA at 07:33, 7 December 2011

OCA — Wed, 07 Dec 2011 07:33:01 GMT

←Older revision		Revision as of 07:33, 7 December 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3u3q is ON HOLD	+	The entry 3u3q is ON HOLD until Paper Publication

	Authors: Ru, H., Zhao, L.X., Ding, W., Jiao, L.Y., Shaw, N., Zhang, L.G., Hung, L.W., Matsugaki, N., Wakatsuki, S., Liu, Z.J.		Authors: Ru, H., Zhao, L.X., Ding, W., Jiao, L.Y., Shaw, N., Zhang, L.G., Hung, L.W., Matsugaki, N., Wakatsuki, S., Liu, Z.J.

	Description: The S-SAD phased crystal structure of Death Receptor 6 (DR6) and its solution conformation revealed by SAXS		Description: The S-SAD phased crystal structure of Death Receptor 6 (DR6) and its solution conformation revealed by SAXS

OCA: Protected "3u3q" [edit=sysop:move=sysop]

OCA — Sun, 30 Oct 2011 08:49:57 GMT

Protected "3u3q" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:49, 30 October 2011

OCA: New page: '''Unreleased structure''' The entry 3u3q is ON HOLD Authors: Ru, H., Zhao, L.X., Ding, W., Jiao, L.Y., Shaw, N., Zhang, L.G., Hung, L.W., Matsugaki, N., Wakatsuki, S., Liu, Z.J. Descr...

OCA — Sun, 30 Oct 2011 08:49:56 GMT

New page: '''Unreleased structure''' The entry 3u3q is ON HOLD Authors: Ru, H., Zhao, L.X., Ding, W., Jiao, L.Y., Shaw, N., Zhang, L.G., Hung, L.W., Matsugaki, N., Wakatsuki, S., Liu, Z.J. Descr...

New page

'''Unreleased structure'''

The entry 3u3q is ON HOLD

Authors: Ru, H., Zhao, L.X., Ding, W., Jiao, L.Y., Shaw, N., Zhang, L.G., Hung, L.W., Matsugaki, N., Wakatsuki, S., Liu, Z.J.

Description: The S-SAD phased crystal structure of Death Receptor 6 (DR6) and its solution conformation revealed by SAXS