6qk9 - Revision history

OCA at 12:02, 24 January 2024

OCA — Wed, 24 Jan 2024 12:02:39 GMT

←Older revision		Revision as of 12:02, 24 January 2024
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	<StructureSection load='6qk9' size='340' side='right'caption='[[6qk9]], [[Resolution\|resolution]] 2.23Å' scene=''>		<StructureSection load='6qk9' size='340' side='right'caption='[[6qk9]], [[Resolution\|resolution]] 2.23Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qk9]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QK9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6QK9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qk9]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QK9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QK9 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=6qk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qk9 OCA], [~~http~~://pdbe.org/6qk9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6qk9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6qk9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6qk9 ProSAT]</span></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]] 2.231Å</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=6qk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qk9 OCA], [https://pdbe.org/6qk9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qk9 RCSB], [https://www.ebi.ac.uk/pdbsum/6qk9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qk9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[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/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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6qk9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6qk9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[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: Buetow, L]]	+	[[Category: Buetow L]]
-	[[Category: Gabrielsen, M]]	+	[[Category: Gabrielsen M]]
-	[[Category: Huang~~, D T~~]]	+	[[Category: Huang DT]]
-	[[Category: Kowalczyk, D]]	+	[[Category: Kowalczyk D]]
-	~~[[Category: Dimer]]~~	+
-	~~[[Category: Dimerisation]]~~	+
-	~~[[Category: Signaling protein]]~~	+
-	~~[[Category: Ubiquitin~~]]	+

OCA at 06:27, 24 July 2019

OCA — Wed, 24 Jul 2019 06:27:31 GMT

←Older revision		Revision as of 06:27, 24 July 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6qk9 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==A dimeric ubiquitin formed by a single amino acid substitution==
		+	<StructureSection load='6qk9' size='340' side='right'caption='[[6qk9]], [[Resolution\|resolution]] 2.23Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6qk9]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QK9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QK9 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=6qk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qk9 OCA], [http://pdbe.org/6qk9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qk9 RCSB], [http://www.ebi.ac.uk/pdbsum/6qk9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qk9 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[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 (Ub) is a small protein that post-translationally modifies a variety of substrates in eukaryotic cells to modulate substrate function. The ability of Ub to interact with numerous protein domains makes Ub an attractive scaffold for engineering ubiquitin variants (UbVs) with high target specificity. Previously, we identified a UbV that formed a non-covalent stable dimer via a beta-strand exchange, and in the current work we identified and characterized the minimal substitutions in the primary sequence of Ub required to form a higher ordered complex. Using solution angle scattering and X-ray crystallography, we show that a single substitution of residue Gly10 to either Ala or Val is sufficient to convert Ub from a monomer to a dimer. We also investigate contributions to dimer formation by the residues in the surrounding sequence. These results can be used to develop next-generation phage-display libraries of UbVs to engineer new interfaces for protein recognition.

-	~~Authors~~:	+	Identification and Characterization of Mutations in Ubiquitin Required for Non-covalent Dimer Formation.,Gabrielsen M, Buetow L, Kowalczyk D, Zhang W, Sidhu SS, Huang DT Structure. 2019 Jul 5. pii: S0969-2126(19)30207-2. doi:, 10.1016/j.str.2019.06.008. PMID:31303481<ref>PMID:31303481</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6qk9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Buetow, L]]
		+	[[Category: Gabrielsen, M]]
		+	[[Category: Huang, D T]]
		+	[[Category: Kowalczyk, D]]
		+	[[Category: Dimer]]
		+	[[Category: Dimerisation]]
		+	[[Category: Signaling protein]]
		+	[[Category: Ubiquitin]]

OCA at 05:18, 21 February 2019

OCA — Thu, 21 Feb 2019 05:18:31 GMT

←Older revision		Revision as of 05:18, 21 February 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6qk9 is ON HOLD	+	The entry 6qk9 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6qk9" [edit=sysop:move=sysop]

OCA — Wed, 13 Feb 2019 07:58:57 GMT

Protected "6qk9" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:58, 13 February 2019

OCA: New page: '''Unreleased structure''' The entry 6qk9 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 13 Feb 2019 07:58:55 GMT

New page: '''Unreleased structure''' The entry 6qk9 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6qk9 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]