6cp0 - Revision history

OCA at 15:08, 4 October 2023

OCA — Wed, 04 Oct 2023 15:08:41 GMT

←Older revision		Revision as of 15:08, 4 October 2023
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	<StructureSection load='6cp0' size='340' side='right'caption='[[6cp0]], [[Resolution\|resolution]] 3.01Å' scene=''>		<StructureSection load='6cp0' size='340' side='right'caption='[[6cp0]], [[Resolution\|resolution]] 3.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cp0]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_33152 Atcc 33152~~] and [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CP0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6CP0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cp0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Legionella_pneumophila Legionella pneumophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CP0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CP0 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~UBE2D3~~, ~~UBC5C, UBCH5C (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=9606 HUMAN])~~</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]] 3.01Å</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=6cp0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cp0 OCA], [~~http~~://pdbe.org/6cp0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6cp0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6cp0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6cp0 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=6cp0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cp0 OCA], [https://pdbe.org/6cp0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cp0 RCSB], [https://www.ebi.ac.uk/pdbsum/6cp0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cp0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~UB2D3_HUMAN UB2D3_HUMAN~~]] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-11'-, as well as 'Lys-48'-linked polyubiquitination. Cooperates with the E2 CDC34 and the SCF(FBXW11) E3 ligase complex for the polyubiquitination of NFKBIA leading to its subsequent proteasomal degradation. Acts as an initiator E2, priming the phosphorylated NFKBIA target at positions 'Lys-21' and/or 'Lys-22' with a monoubiquitin. Ubiquitin chain elongation is then performed by CDC34, building ubiquitin chains from the UBE2D3-primed NFKBIA-linked ubiquitin. Acts also as an initiator E2, in conjunction with RNF8, for the priming of PCNA. Monoubiquitination of PCNA, and its subsequent polyubiquitination, are essential events in the operation of the DNA damage tolerance (DDT) pathway that is activated after DNA damage caused by UV or chemical agents during S-phase. Associates with the BRCA1/BARD1 E3 ligase complex to perform ubiquitination at DNA damage sites following ionizing radiation leading to DNA repair. Targets DAPK3 for ubiquitination which influences promyelocytic leukemia protein nuclear body (PML-NB) formation in the nucleus. In conjunction with the MDM2 and TOPORS E3 ligases, functions ubiquitination of p53/TP53. Supports NRDP1-mediated ubiquitination and degradation of ERBB3 and of BRUCE which triggers apoptosis. In conjunction with the CBL E3 ligase, targets EGFR for polyubiquitination at the plasma membrane as well as during its internalization and transport on endosomes. In conjunction with the STUB1 E3 quality control E3 ligase, ubiquitinates unfolded proteins to catalyze their immediate destruction (By similarity).<ref>PMID:10329681</ref> <ref>PMID:11743028</ref> <ref>PMID:12646252</ref> <ref>PMID:15247280</ref> <ref>PMID:15280377</ref> <ref>PMID:15496420</ref> <ref>PMID:16628214</ref> <ref>PMID:18515077</ref> <ref>PMID:18948756</ref> <ref>PMID:18508924</ref> <ref>PMID:18284575</ref> <ref>PMID:20061386</ref> <ref>PMID:20347421</ref> <ref>PMID:21532592</ref>	+	[https://www.uniprot.org/uniprot/Q6RCR3_LEGPN Q6RCR3_LEGPN]
	<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 6cp0" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6cp0" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[3D structures of ubiquitin conjugating enzyme\|3D structures of ubiquitin conjugating enzyme]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 33152]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Huang, Q~~]]	+	[[Category: Legionella pneumophila]]
-	[[Category: ~~Mao, Y~~]]	+	[[Category: Huang Q]]
-	[[Category: ~~Wasilko, D J~~]]	+	[[Category: Mao Y]]
-	[[Category: ~~Bacterial e3 ligase]]~~	+	[[Category: Wasilko DJ]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: E2]]~~	+
-	~~[[Category: Ligase~~]]	+

OCA at 10:48, 1 January 2020

OCA — Wed, 01 Jan 2020 10:48:28 GMT

←Older revision		Revision as of 10:48, 1 January 2020
Line 1:		Line 1:

	==SdcA in complex with the E2, UbcH5C==		==SdcA in complex with the E2, UbcH5C==
-	<StructureSection load='6cp0' size='340' side='right' caption='[[6cp0]], [[Resolution\|resolution]] 3.01Å' scene=''>	+	<StructureSection load='6cp0' size='340' side='right'caption='[[6cp0]], [[Resolution\|resolution]] 3.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6cp0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33152 Atcc 33152] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CP0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CP0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6cp0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33152 Atcc 33152] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CP0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CP0 FirstGlance]. <br>
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	[[Category: Atcc 33152]]		[[Category: Atcc 33152]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Huang, Q]]		[[Category: Huang, Q]]
	[[Category: Mao, Y]]		[[Category: Mao, Y]]

OCA at 08:33, 21 February 2019

OCA — Thu, 21 Feb 2019 08:33:00 GMT

←Older revision		Revision as of 08:33, 21 February 2019
Line 3:		Line 3:
	<StructureSection load='6cp0' size='340' side='right' caption='[[6cp0]], [[Resolution\|resolution]] 3.01Å' scene=''>		<StructureSection load='6cp0' size='340' side='right' caption='[[6cp0]], [[Resolution\|resolution]] 3.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cp0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CP0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CP0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cp0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33152 Atcc 33152] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CP0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CP0 FirstGlance]. <br>
-	</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=6cp0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cp0 OCA], [http://pdbe.org/6cp0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cp0 RCSB], [http://www.ebi.ac.uk/pdbsum/6cp0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cp0 ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBE2D3, UBC5C, UBCH5C ([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=6cp0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cp0 OCA], [http://pdbe.org/6cp0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cp0 RCSB], [http://www.ebi.ac.uk/pdbsum/6cp0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cp0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 33152]]
		+	[[Category: Human]]
	[[Category: Huang, Q]]		[[Category: Huang, Q]]
	[[Category: Mao, Y]]		[[Category: Mao, Y]]

OCA at 18:47, 1 August 2018

OCA — Wed, 01 Aug 2018 18:47:48 GMT

←Older revision		Revision as of 18:47, 1 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6cp0 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==SdcA in complex with the E2, UbcH5C==
		+	<StructureSection load='6cp0' size='340' side='right' caption='[[6cp0]], [[Resolution\|resolution]] 3.01Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6cp0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CP0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CP0 FirstGlance]. <br>
		+	</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=6cp0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cp0 OCA], [http://pdbe.org/6cp0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cp0 RCSB], [http://www.ebi.ac.uk/pdbsum/6cp0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cp0 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UB2D3_HUMAN UB2D3_HUMAN]] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-11'-, as well as 'Lys-48'-linked polyubiquitination. Cooperates with the E2 CDC34 and the SCF(FBXW11) E3 ligase complex for the polyubiquitination of NFKBIA leading to its subsequent proteasomal degradation. Acts as an initiator E2, priming the phosphorylated NFKBIA target at positions 'Lys-21' and/or 'Lys-22' with a monoubiquitin. Ubiquitin chain elongation is then performed by CDC34, building ubiquitin chains from the UBE2D3-primed NFKBIA-linked ubiquitin. Acts also as an initiator E2, in conjunction with RNF8, for the priming of PCNA. Monoubiquitination of PCNA, and its subsequent polyubiquitination, are essential events in the operation of the DNA damage tolerance (DDT) pathway that is activated after DNA damage caused by UV or chemical agents during S-phase. Associates with the BRCA1/BARD1 E3 ligase complex to perform ubiquitination at DNA damage sites following ionizing radiation leading to DNA repair. Targets DAPK3 for ubiquitination which influences promyelocytic leukemia protein nuclear body (PML-NB) formation in the nucleus. In conjunction with the MDM2 and TOPORS E3 ligases, functions ubiquitination of p53/TP53. Supports NRDP1-mediated ubiquitination and degradation of ERBB3 and of BRUCE which triggers apoptosis. In conjunction with the CBL E3 ligase, targets EGFR for polyubiquitination at the plasma membrane as well as during its internalization and transport on endosomes. In conjunction with the STUB1 E3 quality control E3 ligase, ubiquitinates unfolded proteins to catalyze their immediate destruction (By similarity).<ref>PMID:10329681</ref> <ref>PMID:11743028</ref> <ref>PMID:12646252</ref> <ref>PMID:15247280</ref> <ref>PMID:15280377</ref> <ref>PMID:15496420</ref> <ref>PMID:16628214</ref> <ref>PMID:18515077</ref> <ref>PMID:18948756</ref> <ref>PMID:18508924</ref> <ref>PMID:18284575</ref> <ref>PMID:20061386</ref> <ref>PMID:20347421</ref> <ref>PMID:21532592</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The causative agent of Legionnaires' disease, Legionella pneumophila, delivers more than 330 virulent effectors to its host to establish an intracellular membrane-bound organelle called the Legionella containing vacuole. Among the army of Legionella effectors, SidC and its paralog SdcA have been identified as novel bacterial ubiquitin (Ub) E3 ligases. To gain insight into the molecular mechanism of SidC/SdcA as Ub ligases, we determined the crystal structures of a binary complex of the N-terminal catalytic SNL domain of SdcA with its cognate E2 UbcH5C and a ternary complex consisting of the SNL domain of SidC with the Ub-linked E2 UbcH7. These two structures reveal the molecular determinants governing the Ub transfer cascade catalyzed by SidC. Together, our data support a common mechanism in the Ub transfer cascade in which the donor Ub is immobilized with its C-terminal tail locked in an extended conformation, priming the donor Ub for catalysis.

-	~~Authors: Wasilko, D.J~~., ~~Huang~~, Q., Mao, Y.	+	Insights into the ubiquitin transfer cascade catalyzed by the Legionella effector SidC.,Wasilko DJ, Huang Q, Mao Y Elife. 2018 Jul 17;7. pii: 36154. doi: 10.7554/eLife.36154. PMID:30015617<ref>PMID:30015617</ref>

-	~~Description: SdcA in complex with the E2~~, ~~UbcH5C~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 6cp0" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Huang, Q]]		[[Category: Huang, Q]]
	[[Category: Mao, Y]]		[[Category: Mao, Y]]
-	[[Category: Wasilko, D.J]]	+	[[Category: Wasilko, D J]]
		+	[[Category: Bacterial e3 ligase]]
		+	[[Category: Complex]]
		+	[[Category: E2]]
		+	[[Category: Ligase]]

OCA at 04:00, 25 April 2018

OCA — Wed, 25 Apr 2018 04:00:00 GMT

←Older revision		Revision as of 04:00, 25 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6cp0 is ON HOLD	+	The entry 6cp0 is ON HOLD until Paper Publication

	Authors: Wasilko, D.J., Huang, Q., Mao, Y.		Authors: Wasilko, D.J., Huang, Q., Mao, Y.

OCA: Protected "6cp0" [edit=sysop:move=sysop]

OCA — Wed, 21 Mar 2018 06:11:32 GMT

Protected "6cp0" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:11, 21 March 2018

OCA: New page: '''Unreleased structure''' The entry 6cp0 is ON HOLD Authors: Wasilko, D.J., Huang, Q., Mao, Y. Description: SdcA in complex with the E2, UbcH5C Category: Unreleased Structures [[C...

OCA — Wed, 21 Mar 2018 06:11:31 GMT

New page: '''Unreleased structure''' The entry 6cp0 is ON HOLD Authors: Wasilko, D.J., Huang, Q., Mao, Y. Description: SdcA in complex with the E2, UbcH5C Category: Unreleased Structures [[C...

New page

'''Unreleased structure'''

The entry 6cp0 is ON HOLD

Authors: Wasilko, D.J., Huang, Q., Mao, Y.

Description: SdcA in complex with the E2, UbcH5C
[[Category: Unreleased Structures]]
[[Category: Huang, Q]]
[[Category: Mao, Y]]
[[Category: Wasilko, D.J]]