4ocl - Revision history

OCA at 17:09, 20 September 2023

OCA — Wed, 20 Sep 2023 17:09:37 GMT

←Older revision		Revision as of 17:09, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ocl]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Lama_glama Lama glama] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OCL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OCL FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ocl]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Lama_glama Lama glama] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OCL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OCL 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]] 2.4Å</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ocl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ocl OCA], [https://pdbe.org/4ocl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ocl RCSB], [https://www.ebi.ac.uk/pdbsum/4ocl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ocl 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=4ocl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ocl OCA], [https://pdbe.org/4ocl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ocl RCSB], [https://www.ebi.ac.uk/pdbsum/4ocl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ocl ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:16, 25 January 2023

OCA — Wed, 25 Jan 2023 07:16:59 GMT

←Older revision		Revision as of 07:16, 25 January 2023
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	==Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia==		==Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia==
-	<StructureSection load='4ocl' size='340' side='right' caption='[[4ocl]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='4ocl' size='340' side='right'caption='[[4ocl]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ocl]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~] and [~~http~~://en.wikipedia.org/wiki/~~Camelus_glama Camelus glama~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OCL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4OCL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ocl]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Lama_glama Lama glama] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OCL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OCL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4c0v\|4c0v]], [[4b4t\|4b4t]], [[4ocm\|4ocm]], [[4ocn\|4ocn]]</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=4ocl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ocl OCA], [https://pdbe.org/4ocl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ocl RCSB], [https://www.ebi.ac.uk/pdbsum/4ocl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ocl ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">O5360, RPN8, YOR261C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), MPR1, RPN11, YFR004W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=4ocl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ocl OCA], [~~http~~://pdbe.org/4ocl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ocl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ocl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ocl ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RPN8_YEAST RPN8_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.<ref>PMID:9584156</ref> [[http://www.uniprot.org/uniprot/RPN11_YEAST RPN11_YEAST]] Acts as a regulatory subunit of the 26 proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.<ref>PMID:21075847</ref>	+	[https://www.uniprot.org/uniprot/RPN8_YEAST RPN8_YEAST] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.<ref>PMID:9584156</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 20:

	==See Also==		==See Also==
-	*[[Proteasome\|Proteasome]]	+	*[[Proteasome 3D structures\|Proteasome 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Baker's yeast]]~~	+	[[Category: Lama glama]]
-	~~[[Category: Camelus~~ glama]]	+	[[Category: Large Structures]]
-	[[Category: ~~Bracher, A~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: ~~Pathare, G R~~]]	+	[[Category: Bracher A]]
-	[[Category: ~~26s proteasome~~]]	+	[[Category: Pathare GR]]
-	[[Category: ~~Hydrolase]]~~	+
-	~~[[Category: Isopeptidase activity]]~~	+
-	~~[[Category: Lid]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Regulatory particle]]~~	+
-	~~[[Category: Ubiquitin~~]]	+

OCA at 17:57, 4 August 2016

OCA — Thu, 04 Aug 2016 17:57:50 GMT

←Older revision		Revision as of 17:57, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia==		==Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia==
	<StructureSection load='4ocl' size='340' side='right' caption='[[4ocl]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4ocl' size='340' side='right' caption='[[4ocl]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4c0v\|4c0v]], [[4b4t\|4b4t]], [[4ocm\|4ocm]], [[4ocn\|4ocn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4c0v\|4c0v]], [[4b4t\|4b4t]], [[4ocm\|4ocm]], [[4ocn\|4ocn]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">O5360, RPN8, YOR261C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), MPR1, RPN11, YFR004W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">O5360, RPN8, YOR261C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), MPR1, RPN11, YFR004W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=4ocl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ocl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ocl RCSB], [http://www.ebi.ac.uk/pdbsum/4ocl 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=4ocl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ocl OCA], [http://pdbe.org/4ocl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ocl RCSB], [http://www.ebi.ac.uk/pdbsum/4ocl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ocl 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 4ocl" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 17:54, 24 December 2014

OCA — Wed, 24 Dec 2014 17:54:56 GMT

←Older revision		Revision as of 17:54, 24 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4ocl\| PDB=4ocl \| SCENE= }}~~	+	==Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia==
-	===Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia===	+	<StructureSection load='4ocl' size='340' side='right' caption='[[4ocl]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24516147}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4ocl]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] and [http://en.wikipedia.org/wiki/Camelus_glama Camelus glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OCL FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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">[[4c0v\|4c0v]], [[4b4t\|4b4t]], [[4ocm\|4ocm]], [[4ocn\|4ocn]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">O5360, RPN8, YOR261C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), MPR1, RPN11, YFR004W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=4ocl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ocl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ocl RCSB], [http://www.ebi.ac.uk/pdbsum/4ocl PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/RPN8_YEAST RPN8_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.<ref>PMID:9584156</ref> [[http://www.uniprot.org/uniprot/RPN11_YEAST RPN11_YEAST]] Acts as a regulatory subunit of the 26 proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.<ref>PMID:21075847</ref>		[[http://www.uniprot.org/uniprot/RPN8_YEAST RPN8_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.<ref>PMID:9584156</ref> [[http://www.uniprot.org/uniprot/RPN11_YEAST RPN11_YEAST]] Acts as a regulatory subunit of the 26 proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.<ref>PMID:21075847</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The ATP-dependent degradation of polyubiquitylated proteins by the 26S proteasome is essential for the maintenance of proteome stability and the regulation of a plethora of cellular processes. Degradation of substrates is preceded by the removal of polyubiquitin moieties through the isopeptidase activity of the subunit Rpn11. Here we describe three crystal structures of the heterodimer of the Mpr1-Pad1-N-terminal domains of Rpn8 and Rpn11, crystallized as a fusion protein in complex with a nanobody. This fusion protein exhibits modest deubiquitylation activity toward a model substrate. Full activation requires incorporation of Rpn11 into the 26S proteasome and is dependent on ATP hydrolysis, suggesting that substrate processing and polyubiquitin removal are coupled. Based on our structures, we propose that premature activation is prevented by the combined effects of low intrinsic ubiquitin affinity, an insertion segment acting as a physical barrier across the substrate access channel, and a conformationally unstable catalytic loop in Rpn11. The docking of the structure into the proteasome EM density revealed contacts of Rpn11 with ATPase subunits, which likely stabilize the active conformation and boost the affinity for the proximal ubiquitin moiety. The narrow space around the Rpn11 active site at the entrance to the ATPase ring pore is likely to prevent erroneous deubiquitylation of folded proteins.
		+
		+	Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11.,Pathare GR, Nagy I, Sledz P, Anderson DJ, Zhou HJ, Pardon E, Steyaert J, Forster F, Bracher A, Baumeister W Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):2984-9. doi:, 10.1073/pnas.1400546111. Epub 2014 Feb 10. PMID:24516147<ref>PMID:24516147</ref>

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4ocl]] is~~ a ~~6 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4OCL OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:024516147</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Proteasome\|Proteasome]]
-	[[Category: Bracher, A.]]	+	== References ==
-	[[Category: Pathare, G R.]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Baker's yeast]]
		+	[[Category: Camelus glama]]
		+	[[Category: Bracher, A]]
		+	[[Category: Pathare, G R]]
	[[Category: 26s proteasome]]		[[Category: 26s proteasome]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 08:45, 19 March 2014

OCA — Wed, 19 Mar 2014 08:45:08 GMT

←Older revision		Revision as of 08:45, 19 March 2014
Line 1:		Line 1:
	{{STRUCTURE_4ocl\| PDB=4ocl \| SCENE= }}		{{STRUCTURE_4ocl\| PDB=4ocl \| SCENE= }}
	===Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia===		===Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia===
		+	{{ABSTRACT_PUBMED_24516147}}

	==Function==		==Function==
Line 9:		Line 10:

	==Reference==		==Reference==
-	<references group="xtra"/><references/>	+	<ref group="xtra">PMID:024516147</ref><references group="xtra"/><references/>
	[[Category: Bracher, A.]]		[[Category: Bracher, A.]]
	[[Category: Pathare, G R.]]		[[Category: Pathare, G R.]]

OCA at 07:52, 29 January 2014

OCA — Wed, 29 Jan 2014 07:52:45 GMT

←Older revision		Revision as of 07:52, 29 January 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4ocl\| PDB=4ocl \| SCENE= }}
		+	===Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia===

-	~~The entry 4ocl~~ is ~~ON HOLD~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/RPN8_YEAST RPN8_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.<ref>PMID:9584156</ref> [[http://www.uniprot.org/uniprot/RPN11_YEAST RPN11_YEAST]] Acts as a regulatory subunit of the 26 proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.<ref>PMID:21075847</ref>

-	~~Authors~~: ~~Pathare, G~~.R.~~, Bracher, A~~.	+	==About this Structure==
		+	[[4ocl]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OCL OCA].

-	~~Description~~: ~~Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer~~, ~~crystal form Ia~~	+	==Reference==
		+	<references group="xtra"/><references/>
		+	[[Category: Bracher, A.]]
		+	[[Category: Pathare, G R.]]
		+	[[Category: 26s proteasome]]
		+	[[Category: Hydrolase]]
		+	[[Category: Isopeptidase activity]]
		+	[[Category: Lid]]
		+	[[Category: Protein binding]]
		+	[[Category: Regulatory particle]]
		+	[[Category: Ubiquitin]]

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

OCA — Wed, 15 Jan 2014 07:46:37 GMT

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

←Older revision

Revision as of 07:46, 15 January 2014

OCA: New page: '''Unreleased structure''' The entry 4ocl is ON HOLD Authors: Pathare, G.R., Bracher, A. Description: Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia

OCA — Wed, 15 Jan 2014 07:46:36 GMT

New page: '''Unreleased structure''' The entry 4ocl is ON HOLD Authors: Pathare, G.R., Bracher, A. Description: Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia

New page

'''Unreleased structure'''

The entry 4ocl is ON HOLD

Authors: Pathare, G.R., Bracher, A.

Description: Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia