5ohv - Revision history

OCA at 16:50, 13 December 2023

2023-12-13T16:50:46Z

←Older revision		Revision as of 16:50, 13 December 2023
Line 3:		Line 3:
	<StructureSection load='5ohv' size='340' side='right'caption='[[5ohv]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5ohv' size='340' side='right'caption='[[5ohv]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ohv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OHV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5OHV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ohv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OHV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OHV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.801Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5ohv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ohv OCA], [~~http~~://pdbe.org/5ohv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ohv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ohv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ohv ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5ohv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ohv OCA], [https://pdbe.org/5ohv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ohv RCSB], [https://www.ebi.ac.uk/pdbsum/5ohv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ohv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/UBC_HUMAN UBC_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/UBC_HUMAN UBC_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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 21:

	==See Also==		==See Also==
-	*[[~~Ubiquitin~~\|~~Ubiquitin~~]]	+	*[[3D structures of ubiquitin\|3D structures of ubiquitin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Komander, D~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Michel, M A~~]]	+	[[Category: Komander D]]
-	[[Category: ~~Affimer]]~~	+	[[Category: Michel MA]]
-	~~[[Category: Cystatin]]~~	+
-	~~[[Category: Signaling protein]]~~	+
-	~~[[Category: Ubiquitin~~]]	+

OCA at 12:23, 26 August 2020

2020-08-26T12:23:37Z

←Older revision		Revision as of 12:23, 26 August 2020
Line 1:		Line 1:

	==K33-specific affimer bound to K33 diUb==		==K33-specific affimer bound to K33 diUb==
-	<StructureSection load='5ohv' size='340' side='right' caption='[[5ohv]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='5ohv' size='340' side='right'caption='[[5ohv]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ohv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OHV OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OHV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ohv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OHV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5OHV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5ohv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ohv OCA], [http://pdbe.org/5ohv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ohv RCSB], [http://www.ebi.ac.uk/pdbsum/5ohv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ohv ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ohv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ohv OCA], [http://pdbe.org/5ohv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ohv RCSB], [http://www.ebi.ac.uk/pdbsum/5ohv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ohv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5ohv" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ohv" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ubiquitin\|Ubiquitin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Komander, D]]		[[Category: Komander, D]]
	[[Category: Michel, M A]]		[[Category: Michel, M A]]

OCA at 09:30, 4 October 2017

2017-10-04T09:30:11Z

←Older revision		Revision as of 09:30, 4 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ohv is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==K33-specific affimer bound to K33 diUb==
		+	<StructureSection load='5ohv' size='340' side='right' caption='[[5ohv]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ohv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OHV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OHV FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5ohv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ohv OCA], [http://pdbe.org/5ohv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ohv RCSB], [http://www.ebi.ac.uk/pdbsum/5ohv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ohv ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UBC_HUMAN UBC_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 ==
		+	Several ubiquitin chain types have remained unstudied, mainly because tools and techniques to detect these posttranslational modifications are scarce. Linkage-specific antibodies have shaped our understanding of the roles and dynamics of polyubiquitin signals but are available for only five out of eight linkage types. We here characterize K6- and K33-linkage-specific "affimer" reagents as high-affinity ubiquitin interactors. Crystal structures of affimers bound to their cognate chain types reveal mechanisms of specificity and a K11 cross-reactivity in the K33 affimer. Structure-guided improvements yield superior affinity reagents suitable for western blotting, confocal fluorescence microscopy and pull-down applications. This allowed us to identify RNF144A and RNF144B as E3 ligases that assemble K6-, K11-, and K48-linked polyubiquitin in vitro. A protocol to enrich K6-ubiquitinated proteins from cells identifies HUWE1 as a main E3 ligase for this chain type, and we show that mitofusin-2 is modified with K6-linked polyubiquitin in a HUWE1-dependent manner.

-	~~Authors~~:	+	Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling.,Michel MA, Swatek KN, Hospenthal MK, Komander D Mol Cell. 2017 Sep 20. pii: S1097-2765(17)30617-2. doi:, 10.1016/j.molcel.2017.08.020. PMID:28943312<ref>PMID:28943312</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5ohv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Komander, D]]
		+	[[Category: Michel, M A]]
		+	[[Category: Affimer]]
		+	[[Category: Cystatin]]
		+	[[Category: Signaling protein]]
		+	[[Category: Ubiquitin]]

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

2017-09-27T12:27:03Z

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

←Older revision

Revision as of 12:27, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5ohv is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2017-09-27T12:27:02Z

New page: '''Unreleased structure''' The entry 5ohv is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5ohv is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]