4gba - Revision history

OCA at 06:46, 26 October 2022

OCA — Wed, 26 Oct 2022 06:46:13 GMT

←Older revision		Revision as of 06:46, 26 October 2022
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	==DCNL complex with N-terminally acetylated NEDD8 E2 peptide==		==DCNL complex with N-terminally acetylated NEDD8 E2 peptide==
-	<StructureSection load='4gba' size='340' side='right' caption='[[4gba]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='4gba' size='340' side='right'caption='[[4gba]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4gba]] is a 4 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=4GBA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4GBA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4gba]] is a 4 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=4GBA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GBA FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=AME:N-ACETYLMETHIONINE'>AME</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AME:N-ACETYLMETHIONINE'>AME</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gao\|4gao]]</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=4gba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gba OCA], [https://pdbe.org/4gba PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gba RCSB], [https://www.ebi.ac.uk/pdbsum/4gba PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gba ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DCUN1D3 ([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=4gba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gba OCA], [~~http~~://pdbe.org/4gba PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4gba RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4gba PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4gba ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DCNL3_HUMAN DCNL3_HUMAN]] Potently stimulates the neddylation of cullin components of SCF-type E3 ubiquitin ligase complexes from the NEDD8-conjugating E2 enzyme UBE2F. Neddylation of cullins play an essential role in the regulation of SCF-type complexes activity.<ref>PMID:23201271</ref> [[http://www.uniprot.org/uniprot/UBE2F_HUMAN UBE2F_HUMAN]] Accepts the ubiquitin-like protein NEDD8 from the UBA3-NAE1 E1 complex and catalyzes its covalent attachment to other proteins. The specific interaction with the E3 ubiquitin ligase RBX2, but not RBX1, suggests that the RBX2-UBE2F complex neddylates specific target proteins, such as CUL5.	+	[https://www.uniprot.org/uniprot/DCNL3_HUMAN DCNL3_HUMAN] Potently stimulates the neddylation of cullin components of SCF-type E3 ubiquitin ligase complexes from the NEDD8-conjugating E2 enzyme UBE2F. Neddylation of cullins play an essential role in the regulation of SCF-type complexes activity.<ref>PMID:23201271</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Bennett, E J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Harper, J W~~]]	+	[[Category: Bennett EJ]]
-	[[Category: ~~Miller, D J~~]]	+	[[Category: Harper JW]]
-	[[Category: ~~Monda, J K~~]]	+	[[Category: Miller DJ]]
-	[[Category: ~~Schulman, B A~~]]	+	[[Category: Monda JK]]
-	[[Category: ~~Scott, D C~~]]	+	[[Category: Schulman BA]]
-	[[Category: ~~E3 ligase]]~~	+	[[Category: Scott DC]]
-	~~[[Category: Ligase-peptide complex~~]]	+

OCA at 15:50, 5 August 2016

OCA — Fri, 05 Aug 2016 15:50:32 GMT

←Older revision		Revision as of 15:50, 5 August 2016
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		+
	==DCNL complex with N-terminally acetylated NEDD8 E2 peptide==		==DCNL complex with N-terminally acetylated NEDD8 E2 peptide==
	<StructureSection load='4gba' size='340' side='right' caption='[[4gba]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4gba' size='340' side='right' caption='[[4gba]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4gba]] is a 4 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=4GBA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GBA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4gba]] is a 4 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=4GBA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GBA FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AME:N-ACETYLMETHIONINE'>AME</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=AME:N-ACETYLMETHIONINE'>AME</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gao\|4gao]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gao\|4gao]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DCUN1D3 ([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">DCUN1D3 ([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=4gba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gba OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gba RCSB], [http://www.ebi.ac.uk/pdbsum/4gba 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=4gba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gba OCA], [http://pdbe.org/4gba PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gba RCSB], [http://www.ebi.ac.uk/pdbsum/4gba PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gba ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4gba" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Bennett, E J]]		[[Category: Bennett, E J]]
	[[Category: Harper, J W]]		[[Category: Harper, J W]]

OCA at 03:44, 25 December 2014

OCA — Thu, 25 Dec 2014 03:44:18 GMT

←Older revision		Revision as of 03:44, 25 December 2014
Line 8:		Line 8:
	<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=4gba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gba OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gba RCSB], [http://www.ebi.ac.uk/pdbsum/4gba 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=4gba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gba OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gba RCSB], [http://www.ebi.ac.uk/pdbsum/4gba PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DCNL3_HUMAN DCNL3_HUMAN]] Potently stimulates the neddylation of cullin components of SCF-type E3 ubiquitin ligase complexes from the NEDD8-conjugating E2 enzyme UBE2F. Neddylation of cullins play an essential role in the regulation of SCF-type complexes activity.<ref>PMID:23201271</ref> [[http://www.uniprot.org/uniprot/UBE2F_HUMAN UBE2F_HUMAN]] Accepts the ubiquitin-like protein NEDD8 from the UBA3-NAE1 E1 complex and catalyzes its covalent attachment to other proteins. The specific interaction with the E3 ubiquitin ligase RBX2, but not RBX1, suggests that the RBX2-UBE2F complex neddylates specific target proteins, such as CUL5.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 09:21, 10 December 2014

OCA — Wed, 10 Dec 2014 09:21:26 GMT

←Older revision		Revision as of 09:21, 10 December 2014
Line 1:		Line 1:
-	[[~~Image:~~4gba.~~png~~\|~~left~~\|~~200px~~]]	+	==DCNL complex with N-terminally acetylated NEDD8 E2 peptide==
		+	<StructureSection load='4gba' size='340' side='right' caption='[[4gba]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4gba]] is a 4 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=4GBA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GBA FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AME:N-ACETYLMETHIONINE'>AME</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gao\|4gao]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DCUN1D3 ([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=4gba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gba OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gba RCSB], [http://www.ebi.ac.uk/pdbsum/4gba PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Little is known about molecular recognition of acetylated N termini, despite prevalence of this modification among eukaryotic cytosolic proteins. We report that the family of human DCN-like (DCNL) co-E3s, which promote ligation of the ubiquitin-like protein NEDD8 to cullin targets, recognizes acetylated N termini of the E2 enzymes UBC12 and UBE2F. Systematic biochemical and biophysical analyses reveal 40- and 10-fold variations in affinities among different DCNL-cullin and DCNL-E2 complexes, contributing to varying efficiencies of different NEDD8 ligation cascades. Structures of DCNL2 and DCNL3 complexes with N-terminally acetylated peptides from UBC12 and UBE2F illuminate a common mechanism by which DCNL proteins recognize N-terminally acetylated E2s and how selectivity for interactions dependent on N-acetyl-methionine are established through side chains recognizing distal residues. Distinct preferences of UBC12 and UBE2F peptides for inhibiting different DCNLs, including the oncogenic DCNL1 protein, suggest it may be possible to develop small molecules blocking specific N-acetyl-methionine-dependent protein interactions.

-	~~{{STRUCTURE_4gba\| PDB=4gba \| SCENE= }}~~	+	Structural Conservation of Distinctive N-terminal Acetylation-Dependent Interactions across a Family of Mammalian NEDD8 Ligation Enzymes.,Monda JK, Scott DC, Miller DJ, Lydeard J, King D, Harper JW, Bennett EJ, Schulman BA Structure. 2012 Nov 27. pii: S0969-2126(12)00409-1. doi:, 10.1016/j.str.2012.10.013. PMID:23201271<ref>PMID:23201271</ref>

-	~~===DCNL complex with N-terminally acetylated NEDD8 E2 peptide===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_23201271}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[4gba]] is a 4 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=4GBA OCA].~~	+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Bennett, E J.]]	+	[[Category: Bennett, E J]]
-	[[Category: Harper, J W.]]	+	[[Category: Harper, J W]]
-	[[Category: Miller, D J.]]	+	[[Category: Miller, D J]]
-	[[Category: Monda, J K.]]	+	[[Category: Monda, J K]]
-	[[Category: Schulman, B A.]]	+	[[Category: Schulman, B A]]
-	[[Category: Scott, D C.]]	+	[[Category: Scott, D C]]
	[[Category: E3 ligase]]		[[Category: E3 ligase]]
	[[Category: Ligase-peptide complex]]		[[Category: Ligase-peptide complex]]

OCA at 10:36, 19 December 2012

OCA — Wed, 19 Dec 2012 10:36:18 GMT

←Older revision		Revision as of 10:36, 19 December 2012
Line 1:		Line 1:
-	[[Image:4gba.~~jpg~~\|left\|200px]]	+	[[Image:4gba.png\|left\|200px]]

	{{STRUCTURE_4gba\| PDB=4gba \| SCENE= }}		{{STRUCTURE_4gba\| PDB=4gba \| SCENE= }}
Line 5:		Line 5:
	===DCNL complex with N-terminally acetylated NEDD8 E2 peptide===		===DCNL complex with N-terminally acetylated NEDD8 E2 peptide===

		+	{{ABSTRACT_PUBMED_23201271}}

	==About this Structure==		==About this Structure==

OCA at 14:38, 28 November 2012

OCA — Wed, 28 Nov 2012 14:38:58 GMT

←Older revision		Revision as of 14:38, 28 November 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4gba.jpg\|left\|200px]]

-	~~The entry~~ 4gba ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4gba\| PDB=4gba \| SCENE= }}

-	~~Authors: Monda, J.K., Scott, D.C., Miller, D.J., Harper, J.W., Bennett, E.J., Schulman, B.A.~~	+	===DCNL complex with N-terminally acetylated NEDD8 E2 peptide===

-	~~Description: DCNL complex~~ with N-~~terminally acetylated NEDD8 E2~~ peptide	+
		+	==About this Structure==
		+	[[4gba]] is a 4 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=4GBA OCA].
		+	[[Category: Homo sapiens]]
		+	[[Category: Bennett, E J.]]
		+	[[Category: Harper, J W.]]
		+	[[Category: Miller, D J.]]
		+	[[Category: Monda, J K.]]
		+	[[Category: Schulman, B A.]]
		+	[[Category: Scott, D C.]]
		+	[[Category: E3 ligase]]
		+	[[Category: Ligase-peptide complex]]

OCA at 13:17, 8 November 2012

OCA — Thu, 08 Nov 2012 13:17:54 GMT

←Older revision		Revision as of 13:17, 8 November 2012
Line 5:		Line 5:
	Authors: Monda, J.K., Scott, D.C., Miller, D.J., Harper, J.W., Bennett, E.J., Schulman, B.A.		Authors: Monda, J.K., Scott, D.C., Miller, D.J., Harper, J.W., Bennett, E.J., Schulman, B.A.

-	Description: DCNL-E2 peptide ~~complex~~	+	Description: DCNL complex with N-terminally acetylated NEDD8 E2 peptide

OCA at 04:49, 12 September 2012

OCA — Wed, 12 Sep 2012 04:49:58 GMT

←Older revision		Revision as of 04:49, 12 September 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4gba is ON HOLD	+	The entry 4gba is ON HOLD until Paper Publication

	Authors: Monda, J.K., Scott, D.C., Miller, D.J., Harper, J.W., Bennett, E.J., Schulman, B.A.		Authors: Monda, J.K., Scott, D.C., Miller, D.J., Harper, J.W., Bennett, E.J., Schulman, B.A.

	Description: DCNL-E2 peptide complex		Description: DCNL-E2 peptide complex

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

OCA — Wed, 01 Aug 2012 05:33:34 GMT

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

←Older revision

Revision as of 05:33, 1 August 2012

OCA: New page: '''Unreleased structure''' The entry 4gba is ON HOLD Authors: Monda, J.K., Scott, D.C., Miller, D.J., Harper, J.W., Bennett, E.J., Schulman, B.A. Description: DCNL-E2 peptide complex

OCA — Wed, 01 Aug 2012 05:33:33 GMT

New page: '''Unreleased structure''' The entry 4gba is ON HOLD Authors: Monda, J.K., Scott, D.C., Miller, D.J., Harper, J.W., Bennett, E.J., Schulman, B.A. Description: DCNL-E2 peptide complex

New page

'''Unreleased structure'''

The entry 4gba is ON HOLD

Authors: Monda, J.K., Scott, D.C., Miller, D.J., Harper, J.W., Bennett, E.J., Schulman, B.A.

Description: DCNL-E2 peptide complex