6ob1 - Revision history

OCA at 07:36, 1 May 2024

2024-05-01T07:36:39Z

←Older revision		Revision as of 07:36, 1 May 2024
Line 1:		Line 1:

	==Structure of WHB in complex with Ubiquitin Variant==		==Structure of WHB in complex with Ubiquitin Variant==
-	<StructureSection load='6ob1' size='340' side='right'caption='[[6ob1~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='6ob1' size='340' side='right'caption='[[6ob1]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ob1]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OB1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6OB1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ob1]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OB1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OB1 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ANAPC2, APC2, KIAA1406 ([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">Solution NMR</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=6ob1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ob1 OCA], [~~http~~://pdbe.org/6ob1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ob1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ob1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ob1 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=6ob1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ob1 OCA], [https://pdbe.org/6ob1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ob1 RCSB], [https://www.ebi.ac.uk/pdbsum/6ob1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ob1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ANC2_HUMAN ANC2_HUMAN]] Together with the RING-H2 protein ANAPC11, constitutes the catalytic component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. The APC/C complex acts by mediating ubiquitination and subsequent degradation of target proteins: it mainly mediates the formation of 'Lys-11'-linked polyubiquitin chains and, to a lower extent, the formation of 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains. The CDC20-APC/C complex positively regulates the formation of synaptic vesicle clustering at active zone to the presynaptic membrane in postmitotic neurons. CDC20-APC/C-induced degradation of NEUROD2 drives presynaptic differentiation.<ref>PMID:11739784</ref> <ref>PMID:18485873</ref>	+	[https://www.uniprot.org/uniprot/ANC2_HUMAN ANC2_HUMAN] Together with the RING-H2 protein ANAPC11, constitutes the catalytic component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. The APC/C complex acts by mediating ubiquitination and subsequent degradation of target proteins: it mainly mediates the formation of 'Lys-11'-linked polyubiquitin chains and, to a lower extent, the formation of 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains. The CDC20-APC/C complex positively regulates the formation of synaptic vesicle clustering at active zone to the presynaptic membrane in postmitotic neurons. CDC20-APC/C-induced degradation of NEUROD2 drives presynaptic differentiation.<ref>PMID:11739784</ref> <ref>PMID:18485873</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Ubiquitin (Ub)-mediated proteolysis is a fundamental mechanism used by eukaryotic cells to maintain homeostasis and protein quality, and to control timing in biological processes. Two essential aspects of Ub regulation are conjugation through E1-E2-E3 enzymatic cascades and recognition by Ub-binding domains. An emerging theme in the Ub field is that these 2 properties are often amalgamated in conjugation enzymes. In addition to covalent thioester linkage to Ub's C terminus for Ub transfer reactions, conjugation enzymes often bind noncovalently and weakly to Ub at "exosites." However, identification of such sites is typically empirical and particularly challenging in large molecular machines. Here, studying the 1.2-MDa E3 ligase anaphase-promoting complex/cyclosome (APC/C), which controls cell division and many aspects of neurobiology, we discover a method for identifying unexpected Ub-binding sites. Using a panel of Ub variants (UbVs), we identify a protein-based inhibitor that blocks Ub ligation to APC/C substrates in vitro and ex vivo. Biochemistry, NMR, and cryo-electron microscopy (cryo-EM) structurally define the UbV interaction, explain its inhibitory activity through binding the surface on the APC2 subunit that recruits the E2 enzyme UBE2C, and ultimately reveal that this APC2 surface is also a Ub-binding exosite with preference for K48-linked chains. The results provide a tool for probing APC/C activity, have implications for the coordination of K48-linked Ub chain binding by APC/C with the multistep process of substrate polyubiquitylation, and demonstrate the power of UbV technology for identifying cryptic Ub-binding sites within large multiprotein complexes.	+

-	~~Protein engineering~~ of a ubiquitin~~-variant inhibitor~~ of ~~APC/C identifies a cryptic K48~~ ubiquitin chain binding site.,Watson ER, Grace CRR, Zhang W, Miller DJ, Davidson IF, Prabu JR, Yu S, Bolhuis DL, Kulko ET, Vollrath R, Haselbach D, Stark H, Peters JM, Brown NG, Sidhu SS, Schulman BA Proc Natl Acad Sci U S A. 2019 Jul 26. pii: 1902889116. doi:, 10.1073/pnas.1902889116. PMID:31350353<ref>PMID:31350353</ref>	+	==See Also==
-		+	*[[3D structures of ubiquitin\|3D structures of ubiquitin]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6ob1" style="background-color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Edmond~~, R W~~]]	+	[[Category: Edmond RW]]
-	[[Category: Grace~~, C R]]~~	+	[[Category: Grace CR]]
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Ubiquitin]]~~	+
-	~~[[Category: Whb~~]]	+

OCA at 11:56, 18 December 2019

2019-12-18T11:56:33Z

←Older revision		Revision as of 11:56, 18 December 2019
Line 3:		Line 3:
	<StructureSection load='6ob1' size='340' side='right'caption='[[6ob1]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='6ob1' size='340' side='right'caption='[[6ob1]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ob1]] is a 3 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OB1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OB1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ob1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OB1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OB1 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=6ob1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ob1 OCA], [http://pdbe.org/6ob1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ob1 RCSB], [http://www.ebi.ac.uk/pdbsum/6ob1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ob1 ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ANAPC2, APC2, KIAA1406 ([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=6ob1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ob1 OCA], [http://pdbe.org/6ob1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ob1 RCSB], [http://www.ebi.ac.uk/pdbsum/6ob1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ob1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Edmond, R W]]		[[Category: Edmond, R W]]

OCA at 16:41, 14 August 2019

2019-08-14T16:41:39Z

←Older revision		Revision as of 16:41, 14 August 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ob1 is ~~ON HOLD~~	+	==Structure of WHB in complex with Ubiquitin Variant==
		+	<StructureSection load='6ob1' size='340' side='right'caption='[[6ob1]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6ob1]] is a 3 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OB1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OB1 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=6ob1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ob1 OCA], [http://pdbe.org/6ob1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ob1 RCSB], [http://www.ebi.ac.uk/pdbsum/6ob1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ob1 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ANC2_HUMAN ANC2_HUMAN]] Together with the RING-H2 protein ANAPC11, constitutes the catalytic component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. The APC/C complex acts by mediating ubiquitination and subsequent degradation of target proteins: it mainly mediates the formation of 'Lys-11'-linked polyubiquitin chains and, to a lower extent, the formation of 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains. The CDC20-APC/C complex positively regulates the formation of synaptic vesicle clustering at active zone to the presynaptic membrane in postmitotic neurons. CDC20-APC/C-induced degradation of NEUROD2 drives presynaptic differentiation.<ref>PMID:11739784</ref> <ref>PMID:18485873</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ubiquitin (Ub)-mediated proteolysis is a fundamental mechanism used by eukaryotic cells to maintain homeostasis and protein quality, and to control timing in biological processes. Two essential aspects of Ub regulation are conjugation through E1-E2-E3 enzymatic cascades and recognition by Ub-binding domains. An emerging theme in the Ub field is that these 2 properties are often amalgamated in conjugation enzymes. In addition to covalent thioester linkage to Ub's C terminus for Ub transfer reactions, conjugation enzymes often bind noncovalently and weakly to Ub at "exosites." However, identification of such sites is typically empirical and particularly challenging in large molecular machines. Here, studying the 1.2-MDa E3 ligase anaphase-promoting complex/cyclosome (APC/C), which controls cell division and many aspects of neurobiology, we discover a method for identifying unexpected Ub-binding sites. Using a panel of Ub variants (UbVs), we identify a protein-based inhibitor that blocks Ub ligation to APC/C substrates in vitro and ex vivo. Biochemistry, NMR, and cryo-electron microscopy (cryo-EM) structurally define the UbV interaction, explain its inhibitory activity through binding the surface on the APC2 subunit that recruits the E2 enzyme UBE2C, and ultimately reveal that this APC2 surface is also a Ub-binding exosite with preference for K48-linked chains. The results provide a tool for probing APC/C activity, have implications for the coordination of K48-linked Ub chain binding by APC/C with the multistep process of substrate polyubiquitylation, and demonstrate the power of UbV technology for identifying cryptic Ub-binding sites within large multiprotein complexes.

-	~~Authors~~:	+	Protein engineering of a ubiquitin-variant inhibitor of APC/C identifies a cryptic K48 ubiquitin chain binding site.,Watson ER, Grace CRR, Zhang W, Miller DJ, Davidson IF, Prabu JR, Yu S, Bolhuis DL, Kulko ET, Vollrath R, Haselbach D, Stark H, Peters JM, Brown NG, Sidhu SS, Schulman BA Proc Natl Acad Sci U S A. 2019 Jul 26. pii: 1902889116. doi:, 10.1073/pnas.1902889116. PMID:31350353<ref>PMID:31350353</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6ob1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Edmond, R W]]
		+	[[Category: Grace, C R]]
		+	[[Category: Protein binding]]
		+	[[Category: Ubiquitin]]
		+	[[Category: Whb]]

OCA: Protected "6ob1" [edit=sysop:move=sysop]

2019-03-27T05:04:40Z

Protected "6ob1" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:04, 27 March 2019

OCA: New page: '''Unreleased structure''' The entry 6ob1 is ON HOLD Authors: Description: Category: Unreleased Structures

2019-03-27T05:04:39Z

New page: '''Unreleased structure''' The entry 6ob1 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6ob1 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]