6sqs - Revision history

OCA at 12:46, 24 January 2024

2024-01-24T12:46:09Z

←Older revision		Revision as of 12:46, 24 January 2024
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	<StructureSection load='6sqs' size='340' side='right'caption='[[6sqs]], [[Resolution\|resolution]] 1.83Å' scene=''>		<StructureSection load='6sqs' size='340' side='right'caption='[[6sqs]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6sqs]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cat Cat~~] and [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SQS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6SQS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6sqs]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Felis_catus Felis catus] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SQS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SQS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.83Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6sqo\|6sqo]]~~, ~~[[6sqp\|6sqp]], [[6sqr\|6sqr]]~~<~~/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=6sqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sqs OCA], [https://pdbe.org/6sqs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6sqs RCSB], [https://www.ebi.ac.uk/pdbsum/6sqs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6sqs ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:]]</b></td><td class="sblockDat">MDM2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9685 Cat]), UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RPS27A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+
-	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:~~</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27] </span></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6sqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sqs OCA], [~~http~~://pdbe.org/6sqs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6sqs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6sqs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6sqs ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MDM2_FELCA MDM2_FELCA]] E3 ubiquitin-protein ligase that mediates ubiquitination of p53/TP53, leading to its degradation by the proteasome. Inhibits p53/TP53- and p73/TP73-mediated cell cycle arrest and apoptosis by binding its transcriptional activation domain. Also acts as a ubiquitin ligase E3 toward itself and ARRB1. Permits the nuclear export of p53/TP53. Promotes proteasome-dependent ubiquitin-independent degradation of retinoblastoma RB1 protein. Inhibits DAXX-mediated apoptosis by inducing its ubiquitination and degradation. Component of the TRIM28/KAP1-MDM2-p53/TP53 complex involved in stabilizing p53/TP53. Also component of the TRIM28/KAP1-ERBB4-MDM2 complex which links growth factor and DNA damage response pathways. Mediates ubiquitination and subsequent proteasome degradation of DYRK2 in nucleus. Ubiquitinates IGF1R and SNAI1 and promotes them to proteasomal degradation. Ubiquitinates DCX, leading to DCX degradation and reduction of the dendritic spine density of olfactory bulb granule cells. Ubiquitinates DLG4, leading to proteasomal degradation of DLG4 which is required for AMPA receptor endocytosis.[UniProtKB:P23804][UniProtKB:Q00987] [[http://www.uniprot.org/uniprot/UB2D2_HUMAN UB2D2_HUMAN]] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-48'-linked polyubiquitination. Mediates the selective degradation of short-lived and abnormal proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Mediates ubiquitination of PEX5 and autoubiquitination of STUB1 and TRAF6. Involved in the signal-induced conjugation and subsequent degradation of NFKBIA, FBXW2-mediated GCM1 ubiquitination and degradation, MDM2-dependent degradation of p53/TP53 and the activation of MAVS in the mitochondria by DDX58/RIG-I in response to viral infection. Essential for viral activation of IRF3.<ref>PMID:10329681</ref> <ref>PMID:15280377</ref> <ref>PMID:18042044</ref> <ref>PMID:18703417</ref> <ref>PMID:18359941</ref> <ref>PMID:19854139</ref> <ref>PMID:20403326</ref> <ref>PMID:20061386</ref>	+	[https://www.uniprot.org/uniprot/MDM2_FELCA MDM2_FELCA] E3 ubiquitin-protein ligase that mediates ubiquitination of p53/TP53, leading to its degradation by the proteasome. Inhibits p53/TP53- and p73/TP73-mediated cell cycle arrest and apoptosis by binding its transcriptional activation domain. Also acts as a ubiquitin ligase E3 toward itself and ARRB1. Permits the nuclear export of p53/TP53. Promotes proteasome-dependent ubiquitin-independent degradation of retinoblastoma RB1 protein. Inhibits DAXX-mediated apoptosis by inducing its ubiquitination and degradation. Component of the TRIM28/KAP1-MDM2-p53/TP53 complex involved in stabilizing p53/TP53. Also component of the TRIM28/KAP1-ERBB4-MDM2 complex which links growth factor and DNA damage response pathways. Mediates ubiquitination and subsequent proteasome degradation of DYRK2 in nucleus. Ubiquitinates IGF1R and SNAI1 and promotes them to proteasomal degradation. Ubiquitinates DCX, leading to DCX degradation and reduction of the dendritic spine density of olfactory bulb granule cells. Ubiquitinates DLG4, leading to proteasomal degradation of DLG4 which is required for AMPA receptor endocytosis.[UniProtKB:P23804][UniProtKB:Q00987]
	<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 6sqs" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6sqs" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[MDM2 3D structures\|MDM2 3D structures]]
		+	*[[3D structures of ubiquitin conjugating enzyme\|3D structures of ubiquitin conjugating enzyme]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cat~~]]	+	[[Category: Felis catus]]
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: RING-type E3 ubiquitin transferase]]~~	+	[[Category: Ahmed SF]]
-	[[Category: Ahmed~~, S F~~]]	+	[[Category: Huang DT]]
-	[[Category: Huang~~, D T~~]]	+	[[Category: Magnussen HM]]
-	[[Category: Magnussen~~, H M]]~~	+
-	~~[[Category: E2]]~~	+
-	~~[[Category: E3]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Mdm2]]~~	+
-	~~[[Category: Mdmx]]~~	+
-	~~[[Category: Phosphorylation]]~~	+
-	~~[[Category: Ubiquitin]]~~	+
-	~~[[Category: Ubiquitin ligase~~]]	+

OCA at 05:53, 13 May 2020

2020-05-13T05:53:57Z

←Older revision		Revision as of 05:53, 13 May 2020
Line 1:		Line 1:

	==Crystal structure of cat phospho-Ser429 MDM2 RING domain bound to UbcH5B-Ub==		==Crystal structure of cat phospho-Ser429 MDM2 RING domain bound to UbcH5B-Ub==
-	<StructureSection load='6sqs' size='340' side='right'caption='[[6sqs]]' scene=''>	+	<StructureSection load='6sqs' size='340' side='right'caption='[[6sqs]], [[Resolution\|resolution]] 1.83Å' 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=6SQS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6SQS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6sqs]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Cat Cat] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SQS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6SQS FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6sqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sqs OCA], [http://pdbe.org/6sqs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sqs RCSB], [http://www.ebi.ac.uk/pdbsum/6sqs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sqs ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6sqo\|6sqo]], [[6sqp\|6sqp]], [[6sqr\|6sqr]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MDM2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9685 Cat]), UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RPS27A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6sqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sqs OCA], [http://pdbe.org/6sqs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sqs RCSB], [http://www.ebi.ac.uk/pdbsum/6sqs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sqs ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MDM2_FELCA MDM2_FELCA]] E3 ubiquitin-protein ligase that mediates ubiquitination of p53/TP53, leading to its degradation by the proteasome. Inhibits p53/TP53- and p73/TP73-mediated cell cycle arrest and apoptosis by binding its transcriptional activation domain. Also acts as a ubiquitin ligase E3 toward itself and ARRB1. Permits the nuclear export of p53/TP53. Promotes proteasome-dependent ubiquitin-independent degradation of retinoblastoma RB1 protein. Inhibits DAXX-mediated apoptosis by inducing its ubiquitination and degradation. Component of the TRIM28/KAP1-MDM2-p53/TP53 complex involved in stabilizing p53/TP53. Also component of the TRIM28/KAP1-ERBB4-MDM2 complex which links growth factor and DNA damage response pathways. Mediates ubiquitination and subsequent proteasome degradation of DYRK2 in nucleus. Ubiquitinates IGF1R and SNAI1 and promotes them to proteasomal degradation. Ubiquitinates DCX, leading to DCX degradation and reduction of the dendritic spine density of olfactory bulb granule cells. Ubiquitinates DLG4, leading to proteasomal degradation of DLG4 which is required for AMPA receptor endocytosis.[UniProtKB:P23804][UniProtKB:Q00987] [[http://www.uniprot.org/uniprot/UB2D2_HUMAN UB2D2_HUMAN]] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-48'-linked polyubiquitination. Mediates the selective degradation of short-lived and abnormal proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Mediates ubiquitination of PEX5 and autoubiquitination of STUB1 and TRAF6. Involved in the signal-induced conjugation and subsequent degradation of NFKBIA, FBXW2-mediated GCM1 ubiquitination and degradation, MDM2-dependent degradation of p53/TP53 and the activation of MAVS in the mitochondria by DDX58/RIG-I in response to viral infection. Essential for viral activation of IRF3.<ref>PMID:10329681</ref> <ref>PMID:15280377</ref> <ref>PMID:18042044</ref> <ref>PMID:18703417</ref> <ref>PMID:18359941</ref> <ref>PMID:19854139</ref> <ref>PMID:20403326</ref> <ref>PMID:20061386</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phosphorylation of MDM2 by ATM upon DNA damage is an important mechanism for deregulating MDM2, thereby leading to p53 activation. ATM phosphorylates multiple residues near the RING domain of MDM2, but the underlying molecular basis for deregulation remains elusive. Here we show that Ser429 phosphorylation selectively enhances the ubiquitin ligase activity of MDM2 homodimer but not MDM2-MDMX heterodimer. A crystal structure of phospho-Ser429 (pS429)-MDM2 bound to E2-ubiquitin reveals a unique 310-helical feature present in MDM2 homodimer that allows pS429 to stabilize the closed E2-ubiquitin conformation and thereby enhancing ubiquitin transfer. In cells Ser429 phosphorylation increases MDM2 autoubiquitination and degradation upon DNA damage, whereas S429A substitution protects MDM2 from auto-degradation. Our results demonstrate that Ser429 phosphorylation serves as a switch to boost the activity of MDM2 homodimer and promote its self-destruction to enable rapid p53 stabilization and resolve a long-standing controversy surrounding MDM2 auto-degradation in response to DNA damage.
		+
		+	Structural basis for DNA damage-induced phosphoregulation of MDM2 RING domain.,Magnussen HM, Ahmed SF, Sibbet GJ, Hristova VA, Nomura K, Hock AK, Archibald LJ, Jamieson AG, Fushman D, Vousden KH, Weissman AM, Huang DT Nat Commun. 2020 Apr 29;11(1):2094. doi: 10.1038/s41467-020-15783-y. PMID:32350255<ref>PMID:32350255</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6sqs" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cat]]
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ahmed SF]]	+	[[Category: RING-type E3 ubiquitin transferase]]
-	[[Category: Huang DT]]	+	[[Category: Ahmed, S F]]
-	[[Category: Magnussen HM]]	+	[[Category: Huang, D T]]
		+	[[Category: Magnussen, H M]]
		+	[[Category: E2]]
		+	[[Category: E3]]
		+	[[Category: Ligase]]
		+	[[Category: Mdm2]]
		+	[[Category: Mdmx]]
		+	[[Category: Phosphorylation]]
		+	[[Category: Ubiquitin]]
		+	[[Category: Ubiquitin ligase]]

OCA at 06:03, 6 May 2020

2020-05-06T06:03:00Z

←Older revision		Revision as of 06:03, 6 May 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6sqs is ~~ON HOLD~~	+	==Crystal structure of cat phospho-Ser429 MDM2 RING domain bound to UbcH5B-Ub==
-		+	<StructureSection load='6sqs' size='340' side='right'caption='[[6sqs]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SQS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6SQS FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6sqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sqs OCA], [http://pdbe.org/6sqs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sqs RCSB], [http://www.ebi.ac.uk/pdbsum/6sqs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sqs ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ahmed SF]]
		+	[[Category: Huang DT]]
		+	[[Category: Magnussen HM]]

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

2019-10-02T07:37:06Z

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

←Older revision

Revision as of 07:37, 2 October 2019

OCA: New page: '''Unreleased structure''' The entry 6sqs is ON HOLD Authors: Description: Category: Unreleased Structures

2019-10-02T07:37:04Z

New page: '''Unreleased structure''' The entry 6sqs is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6sqs is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]