6kgi - Revision history

OCA at 10:33, 22 November 2023

OCA — Wed, 22 Nov 2023 10:33:12 GMT

←Older revision		Revision as of 10:33, 22 November 2023
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	<StructureSection load='6kgi' size='340' side='right'caption='[[6kgi]], [[Resolution\|resolution]] 1.04Å' scene=''>		<StructureSection load='6kgi' size='340' side='right'caption='[[6kgi]], [[Resolution\|resolution]] 1.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kgi]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KGI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6KGI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kgi]] is a 1 chain structure with sequence from [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=6KGI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KGI 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='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.04Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">UBR1, PTR1, YGR184C, G7168 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=559292 Baker's yeast])~~</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='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27]~~ </~~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=6kgi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kgi OCA], [https://pdbe.org/6kgi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kgi RCSB], [https://www.ebi.ac.uk/pdbsum/6kgi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kgi ProSAT]</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=6kgi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kgi OCA], [~~http~~://pdbe.org/6kgi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kgi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kgi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kgi ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/UBR1_YEAST UBR1_YEAST]] Ubiquitin ligase protein which is a component of the N-end rule pathway. Recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation.	+	[https://www.uniprot.org/uniprot/UBR1_YEAST UBR1_YEAST] Ubiquitin ligase protein which is a component of the N-end rule pathway. Recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6kgi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6kgi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ubiquitin protein ligase 3D structures\|Ubiquitin protein ligase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~RING-type E3 ubiquitin transferase~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: Heo, J]]	+	[[Category: Heo J]]
-	[[Category: Kim, L]]	+	[[Category: Kim L]]
-	[[Category: Kwon~~, D H~~]]	+	[[Category: Kwon DH]]
-	[[Category: Song~~, H K]]~~	+	[[Category: Song HK]]
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Ubr box]]~~	+
-	~~[[Category: Ubr1~~]]	+

OCA at 07:52, 11 March 2020

OCA — Wed, 11 Mar 2020 07:52:31 GMT

←Older revision		Revision as of 07:52, 11 March 2020
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	<StructureSection load='6kgi' size='340' side='right'caption='[[6kgi]], [[Resolution\|resolution]] 1.04Å' scene=''>		<StructureSection load='6kgi' size='340' side='right'caption='[[6kgi]], [[Resolution\|resolution]] 1.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kgi]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KGI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KGI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kgi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KGI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KGI 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"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBR1, PTR1, YGR184C, G7168 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27] </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=6kgi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kgi OCA], [http://pdbe.org/6kgi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kgi RCSB], [http://www.ebi.ac.uk/pdbsum/6kgi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kgi ProSAT]</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=6kgi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kgi OCA], [http://pdbe.org/6kgi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kgi RCSB], [http://www.ebi.ac.uk/pdbsum/6kgi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kgi ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: RING-type E3 ubiquitin transferase]]		[[Category: RING-type E3 ubiquitin transferase]]

OCA at 16:08, 22 January 2020

OCA — Wed, 22 Jan 2020 16:08:29 GMT

←Older revision		Revision as of 16:08, 22 January 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6kgi is ~~ON HOLD until Paper~~ Publication	+	==RLGS-yUbr1 Ubr box==
		+	<StructureSection load='6kgi' size='340' side='right'caption='[[6kgi]], [[Resolution\|resolution]] 1.04Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6kgi]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KGI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KGI 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>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27] </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=6kgi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kgi OCA], [http://pdbe.org/6kgi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kgi RCSB], [http://www.ebi.ac.uk/pdbsum/6kgi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kgi ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UBR1_YEAST UBR1_YEAST]] Ubiquitin ligase protein which is a component of the N-end rule pathway. Recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The N-degron pathway, formerly the N-end rule pathway, is a protein degradation process that determines the half-life of proteins based on their N-terminal residues. In contrast to the well-established in vivo studies over decades, in vitro studies of this pathway, including biochemical characterization and high-resolution structures, are relatively limited. In this study, we have developed a unique fusion technique using microtubule-associated protein 1A/1B light chain 3B, a key marker protein of autophagy, to tag the N-terminus of the proteins involved in the N-degron pathway, which enables high yield of homogeneous target proteins with variable N-terminal residues for diverse biochemical studies including enzymatic and binding assays and substrate identification. Intriguingly, crystallization showed a markedly enhanced probability, even for the N-degron complexes. To validate our results, we determined the structures of select proteins in the N-degron pathway and compared them to the PDB-deposited proteins. Furthermore, several biochemical applications of this technique were introduced. Therefore, this technique can be used as a general tool for the in vitro study of the N-degron pathway.

-	~~Authors: Heo, J~~., Kwon, ~~D.H.~~, ~~Kim, L.~~, Song~~, H~~.K.	+	Use of the LC3B-fusion technique for biochemical and structural studies of proteins involved in the N-degron pathway.,Kim L, Kwon DH, Heo J, Park MR, Song HK J Biol Chem. 2020 Jan 9. pii: RA119.010912. doi: 10.1074/jbc.RA119.010912. PMID:31919097<ref>PMID:31919097</ref>

-	~~Description: RLGS-yUbr1 Ubr box~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Kwon, D.H]]~~	+	<div class="pdbe-citations 6kgi" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Kim, L~~]]	+	== References ==
-	[[Category: ~~Song, H.K~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: RING-type E3 ubiquitin transferase]]
	[[Category: Heo, J]]		[[Category: Heo, J]]
		+	[[Category: Kim, L]]
		+	[[Category: Kwon, D H]]
		+	[[Category: Song, H K]]
		+	[[Category: Ligase]]
		+	[[Category: Ubr box]]
		+	[[Category: Ubr1]]

OCA at 04:00, 21 August 2019

OCA — Wed, 21 Aug 2019 04:00:39 GMT

←Older revision		Revision as of 04:00, 21 August 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6kgi is ON HOLD	+	The entry 6kgi is ON HOLD until Paper Publication

	Authors: Heo, J., Kwon, D.H., Kim, L., Song, H.K.		Authors: Heo, J., Kwon, D.H., Kim, L., Song, H.K.

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

OCA — Wed, 17 Jul 2019 08:47:21 GMT

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

←Older revision

Revision as of 08:47, 17 July 2019

OCA: New page: '''Unreleased structure''' The entry 6kgi is ON HOLD Authors: Heo, J., Kwon, D.H., Kim, L., Song, H.K. Description: RLGS-yUbr1 Ubr box Category: Unreleased Structures [[Category: K...

OCA — Wed, 17 Jul 2019 08:47:20 GMT

New page: '''Unreleased structure''' The entry 6kgi is ON HOLD Authors: Heo, J., Kwon, D.H., Kim, L., Song, H.K. Description: RLGS-yUbr1 Ubr box Category: Unreleased Structures [[Category: K...

New page

'''Unreleased structure'''

The entry 6kgi is ON HOLD

Authors: Heo, J., Kwon, D.H., Kim, L., Song, H.K.

Description: RLGS-yUbr1 Ubr box
[[Category: Unreleased Structures]]
[[Category: Kwon, D.H]]
[[Category: Kim, L]]
[[Category: Song, H.K]]
[[Category: Heo, J]]