5ln1 - Revision history

OCA at 18:35, 18 October 2023

2023-10-18T18:35:27Z

←Older revision		Revision as of 18:35, 18 October 2023
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	<StructureSection load='5ln1' size='340' side='right'caption='[[5ln1]], [[Resolution\|resolution]] 3.14Å' scene=''>		<StructureSection load='5ln1' size='340' side='right'caption='[[5ln1]], [[Resolution\|resolution]] 3.14Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ln1]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~] and [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LN1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5LN1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ln1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=5LN1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LN1 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~RPN10~~, ~~MCB1, SUN1, YHR200W (~~[~~http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast~~]~~), UBB ([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]] 3.14Å</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=5ln1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ln1 OCA], [~~http~~://pdbe.org/5ln1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ln1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ln1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ln1 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=5ln1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ln1 OCA], [https://pdbe.org/5ln1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ln1 RCSB], [https://www.ebi.ac.uk/pdbsum/5ln1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ln1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RPN10_YEAST RPN10_YEAST]] Multiubiquitin binding protein. [[http://www.uniprot.org/uniprot/UBB_HUMAN UBB_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>	+	[https://www.uniprot.org/uniprot/RPN10_YEAST RPN10_YEAST] Multiubiquitin binding protein.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Proteasome\|Proteasome]]	+	*[[Proteasome 3D structures\|Proteasome 3D structures]]
-	*[[Ubiquitin\|Ubiquitin]]	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Baker's yeast]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Attali, I]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: Keren-Kaplan, T]]	+	[[Category: Attali I]]
-	[[Category: Levin-Kravets, O]]	+	[[Category: Keren-Kaplan T]]
-	[[Category: Prag, G]]	+	[[Category: Levin-Kravets O]]
-	~~[[Category: Proteasome]]~~	+	[[Category: Prag G]]
-	~~[[Category: Ubiquitin]]~~	+
-	~~[[Category: Ubiquitin-binding protein]]~~	+
-	~~[[Category: Ubiquitylation]]~~	+
-	~~[[Category: Vwa~~]]	+

OCA at 13:07, 10 May 2019

2019-05-10T13:07:44Z

←Older revision		Revision as of 13:07, 10 May 2019
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	==STRUCTURE OF UBIQUITYLATED-RPN10 FROM YEAST;==		==STRUCTURE OF UBIQUITYLATED-RPN10 FROM YEAST;==
-	<StructureSection load='5ln1' size='340' side='right' caption='[[5ln1]], [[Resolution\|resolution]] 3.14Å' scene=''>	+	<StructureSection load='5ln1' size='340' side='right'caption='[[5ln1]], [[Resolution\|resolution]] 3.14Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ln1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LN1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LN1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ln1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LN1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LN1 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=5ln1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ln1 OCA], [http://pdbe.org/5ln1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ln1 RCSB], [http://www.ebi.ac.uk/pdbsum/5ln1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ln1 ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RPN10, MCB1, SUN1, YHR200W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), UBB ([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=5ln1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ln1 OCA], [http://pdbe.org/5ln1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ln1 RCSB], [http://www.ebi.ac.uk/pdbsum/5ln1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ln1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5ln1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ln1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Proteasome\|Proteasome]]
		+	*[[Ubiquitin\|Ubiquitin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Attali, I]]		[[Category: Attali, I]]
	[[Category: Keren-Kaplan, T]]		[[Category: Keren-Kaplan, T]]

OCA at 17:18, 19 October 2016

2016-10-19T17:18:41Z

←Older revision		Revision as of 17:18, 19 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ln1 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==STRUCTURE OF UBIQUITYLATED-RPN10 FROM YEAST;==
		+	<StructureSection load='5ln1' size='340' side='right' caption='[[5ln1]], [[Resolution\|resolution]] 3.14Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ln1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LN1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LN1 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=5ln1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ln1 OCA], [http://pdbe.org/5ln1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ln1 RCSB], [http://www.ebi.ac.uk/pdbsum/5ln1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ln1 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RPN10_YEAST RPN10_YEAST]] Multiubiquitin binding protein. [[http://www.uniprot.org/uniprot/UBB_HUMAN UBB_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ubiquitin receptors decode ubiquitin signals into many cellular responses. Ubiquitin receptors also undergo coupled monoubiquitylation, and rapid deubiquitylation has hampered the characterization of the ubiquitylated state. Using bacteria that express a ubiquitylation apparatus, we purified and determined the crystal structure of the proteasomal ubiquitin-receptor Rpn10 in its ubiquitylated state. The structure shows a novel ubiquitin-binding patch that directs K84 ubiquitylation. Superimposition of ubiquitylated-Rpn10 onto electron-microscopy models of proteasomes indicates that the Rpn10-conjugated ubiquitin clashes with Rpn9, suggesting that ubiquitylation might be involved in releasing Rpn10 from the proteasome. Indeed, ubiquitylation on immobilized proteasomes dissociates the modified Rpn10 from the complex, while unmodified Rpn10 mainly remains associated. In vivo experiments indicate that contrary to wild type, Rpn10-K84R is stably associated with the proteasomal subunit Rpn9. Similarly Rpn10, but not ubiquitylated-Rpn10, binds Rpn9 in vitro. Thus we suggest that ubiquitylation functions to dissociate modified ubiquitin receptors from their targets, a function that promotes cyclic activity of ubiquitin receptors.

-	~~Authors:~~ Keren-Kaplan, T., ~~Attali, I.~~, Levin-Kravets, O., ~~Prag~~, G.	+	Structure of ubiquitylated-Rpn10 provides insight into its autoregulation mechanism.,Keren-Kaplan T, Zeev Peters L, Levin-Kravets O, Attali I, Kleifeld O, Shohat N, Artzi S, Zucker O, Pilzer I, Reis N, Glickman MH, Ben-Aroya S, Prag G Nat Commun. 2016 Oct 4;7:12960. doi: 10.1038/ncomms12960. PMID:27698474<ref>PMID:27698474</ref>

-	~~Description: STRUCTURE OF UBIQUITYLATED-RPN10 FROM YEAST~~;	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Prag, G]]~~	+	<div class="pdbe-citations 5ln1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Attali, I]]		[[Category: Attali, I]]
-	[[Category: Levin-Kravets, O]]
	[[Category: Keren-Kaplan, T]]		[[Category: Keren-Kaplan, T]]
		+	[[Category: Levin-Kravets, O]]
		+	[[Category: Prag, G]]
		+	[[Category: Proteasome]]
		+	[[Category: Ubiquitin]]
		+	[[Category: Ubiquitin-binding protein]]
		+	[[Category: Ubiquitylation]]
		+	[[Category: Vwa]]

OCA at 15:03, 9 September 2016

2016-09-09T15:03:09Z

←Older revision		Revision as of 15:03, 9 September 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ln1 is ON HOLD	+	The entry 5ln1 is ON HOLD until Paper Publication

	Authors: Keren-Kaplan, T., Attali, I., Levin-Kravets, O., Prag, G.		Authors: Keren-Kaplan, T., Attali, I., Levin-Kravets, O., Prag, G.

OCA: Protected "5ln1" [edit=sysop:move=sysop]

2016-08-10T14:40:42Z

Protected "5ln1" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:40, 10 August 2016

OCA: New page: '''Unreleased structure''' The entry 5ln1 is ON HOLD Authors: Keren-Kaplan, T., Attali, I., Levin-Kravets, O., Prag, G. Description: STRUCTURE OF UBIQUITYLATED-RPN10 FROM YEAST; [[Cate...

2016-08-10T14:40:40Z

New page: '''Unreleased structure''' The entry 5ln1 is ON HOLD Authors: Keren-Kaplan, T., Attali, I., Levin-Kravets, O., Prag, G. Description: STRUCTURE OF UBIQUITYLATED-RPN10 FROM YEAST; [[Cate...

New page

'''Unreleased structure'''

The entry 5ln1 is ON HOLD

Authors: Keren-Kaplan, T., Attali, I., Levin-Kravets, O., Prag, G.

Description: STRUCTURE OF UBIQUITYLATED-RPN10 FROM YEAST;
[[Category: Unreleased Structures]]
[[Category: Prag, G]]
[[Category: Attali, I]]
[[Category: Levin-Kravets, O]]
[[Category: Keren-Kaplan, T]]