7qo5 - Revision history

OCA at 10:00, 15 March 2023

OCA — Wed, 15 Mar 2023 10:00:54 GMT

←Older revision		Revision as of 10:00, 15 March 2023
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	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PSB2_YEAST PSB2_YEAST]] The proteasome degrades poly-ubiquitinated proteins in the cytoplasm and in the nucleus. It is essential for the regulated turnover of proteins and for the removal of misfolded proteins. The proteasome is a multicatalytic proteinase complex that is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. It has an ATP-dependent proteolytic activity.	+	[https://www.uniprot.org/uniprot/PSB2_YEAST PSB2_YEAST] The proteasome degrades poly-ubiquitinated proteins in the cytoplasm and in the nucleus. It is essential for the regulated turnover of proteins and for the removal of misfolded proteins. The proteasome is a multicatalytic proteinase complex that is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. It has an ATP-dependent proteolytic activity.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 05:25, 8 September 2022

OCA — Thu, 08 Sep 2022 05:25:56 GMT

←Older revision		Revision as of 05:25, 8 September 2022
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-	====	+	==26S proteasome Rpt1-RK -Ubp6-UbVS complex in the si state==
-	<StructureSection load='7qo5' size='340' side='right'caption='[[7qo5]]' scene=''>	+	<StructureSection load='7qo5' size='340' side='right'caption='[[7qo5]], [[Resolution\|resolution]] 6.00Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7qo5]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QO5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QO5 FirstGlance]. <br>
-	</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=7qo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qo5 OCA], [https://pdbe.org/7qo5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qo5 RCSB], [https://www.ebi.ac.uk/pdbsum/7qo5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qo5 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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GLZ:AMINO-ACETALDEHYDE'>GLZ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=7qo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qo5 OCA], [https://pdbe.org/7qo5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qo5 RCSB], [https://www.ebi.ac.uk/pdbsum/7qo5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qo5 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/PSB2_YEAST PSB2_YEAST]] The proteasome degrades poly-ubiquitinated proteins in the cytoplasm and in the nucleus. It is essential for the regulated turnover of proteins and for the removal of misfolded proteins. The proteasome is a multicatalytic proteinase complex that is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. It has an ATP-dependent proteolytic activity.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The proteasome recognizes ubiquitinated proteins and can also edit ubiquitin marks, allowing substrates to be rejected based on ubiquitin chain topology. In yeast, editing is mediated by deubiquitinating enzyme Ubp6. The proteasome activates Ubp6, whereas Ubp6 inhibits the proteasome through deubiquitination and a noncatalytic effect. Here, we report cryo-EM structures of the proteasome bound to Ubp6, based on which we identify mutants in Ubp6 and proteasome subunit Rpt1 that abrogate Ubp6 activation. The Ubp6 mutations define a conserved region that we term the ILR element. The ILR is found within the BL1 loop, which obstructs the catalytic groove in free Ubp6. Rpt1-ILR interaction opens the groove by rearranging not only BL1 but also a previously undescribed network of three interconnected active-site-blocking loops. Ubp6 activation and noncatalytic proteasome inhibition are linked in that they are eliminated by the same mutations. Ubp6 and ubiquitin together drive proteasomes into a unique conformation associated with proteasome inhibition. Thus, a multicomponent allosteric switch exerts simultaneous control over both Ubp6 and the proteasome.
		+
		+	Allosteric control of Ubp6 and the proteasome via a bidirectional switch.,Hung KYS, Klumpe S, Eisele MR, Elsasser S, Tian G, Sun S, Moroco JA, Cheng TC, Joshi T, Seibel T, Van Dalen D, Feng XH, Lu Y, Ovaa H, Engen JR, Lee BH, Rudack T, Sakata E, Finley D Nat Commun. 2022 Feb 11;13(1):838. doi: 10.1038/s41467-022-28186-y. PMID:35149681<ref>PMID:35149681</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7qo5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Saccharomyces cerevisiae]]
		+	[[Category: Cheng TC]]
		+	[[Category: Eisele MR]]
		+	[[Category: Elsasser S]]
		+	[[Category: Finley D]]
		+	[[Category: Geng TT]]
		+	[[Category: Hung KYS]]
		+	[[Category: Joshi T]]
		+	[[Category: Klumpe S]]
		+	[[Category: Rudack T]]
		+	[[Category: Sakata E]]

OCA at 06:16, 16 March 2022

OCA — Wed, 16 Mar 2022 06:16:17 GMT

←Older revision		Revision as of 06:16, 16 March 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7qo5 ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7qo5' size='340' side='right'caption='[[7qo5]]' scene=''>
-	~~Authors~~: ~~Hung, K~~.Y.S.~~, Klumpe, S~~.~~, Eisele, M~~.R.~~, Elsasser, S~~.~~, Geng, T~~.T., ~~Cheng, T~~.C.~~, Joshi, T~~.~~, Rudack, T., Sakata, E., Finley, D.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description: Structure of the 26S proteasome~~-~~Ubp6 complex in the si Rpt1-RK state~~	+	</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=7qo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qo5 OCA], [https://pdbe.org/7qo5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qo5 RCSB], [https://www.ebi.ac.uk/pdbsum/7qo5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qo5 ProSAT]</span></td></tr>
-	~~[[Category: Unreleased Structures~~]]	+	</table>
-	~~[[Category: Sakata~~, ~~E]]~~	+	__TOC__
-	[~~[Category~~: ~~Klumpe, S~~]]	+	</StructureSection>
-	~~[[Category: Joshi~~, ~~T]]~~	+	[[Category: Large Structures]]
-	[~~[Category~~: ~~Rudack, T~~]]	+	[[Category: Z-disk]]
-	~~[[Category: Eisele~~, ~~M.R]]~~	+
-	[~~[Category~~: ~~Geng, T~~.T]]	+
-	~~[[Category: Cheng~~, ~~T.C]]~~	+
-	[~~[Category~~: ~~Hung, K~~.Y.S]]	+
-	[[Category: ~~Finley, D~~]]	+
-	[[Category: ~~Elsasser, S~~]]	+

OCA: Protected "7qo5" [edit=sysop:move=sysop]

OCA — Wed, 29 Dec 2021 11:58:19 GMT

Protected "7qo5" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:58, 29 December 2021

OCA: New page: '''Unreleased structure''' The entry 7qo5 is ON HOLD Authors: Hung, K.Y.S., Klumpe, S., Eisele, M.R., Elsasser, S., Geng, T.T., Cheng, T.C., Joshi, T., Rudack, T., Sakata, E., Finley, D...

OCA — Wed, 29 Dec 2021 11:58:18 GMT

New page: '''Unreleased structure''' The entry 7qo5 is ON HOLD Authors: Hung, K.Y.S., Klumpe, S., Eisele, M.R., Elsasser, S., Geng, T.T., Cheng, T.C., Joshi, T., Rudack, T., Sakata, E., Finley, D...

New page

'''Unreleased structure'''

The entry 7qo5 is ON HOLD

Authors: Hung, K.Y.S., Klumpe, S., Eisele, M.R., Elsasser, S., Geng, T.T., Cheng, T.C., Joshi, T., Rudack, T., Sakata, E., Finley, D.

Description: Structure of the 26S proteasome-Ubp6 complex in the si Rpt1-RK state
[[Category: Unreleased Structures]]
[[Category: Sakata, E]]
[[Category: Klumpe, S]]
[[Category: Joshi, T]]
[[Category: Rudack, T]]
[[Category: Eisele, M.R]]
[[Category: Geng, T.T]]
[[Category: Cheng, T.C]]
[[Category: Hung, K.Y.S]]
[[Category: Finley, D]]
[[Category: Elsasser, S]]