5tog - Revision history

OCA at 13:06, 4 October 2023

2023-10-04T13:06:32Z

←Older revision		Revision as of 13:06, 4 October 2023
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	<StructureSection load='5tog' size='340' side='right'caption='[[5tog]], [[Resolution\|resolution]] 1.08Å' scene=''>		<StructureSection load='5tog' size='340' side='right'caption='[[5tog]], [[Resolution\|resolution]] 1.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tog]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TOG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TOG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tog]] is a 1 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=5TOG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TOG FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><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]] 1.08Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5tof\|5tof]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">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'>[https://proteopedia.org/fgij/fg.htm?mol=5tog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tog OCA], [https://pdbe.org/5tog PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tog RCSB], [https://www.ebi.ac.uk/pdbsum/5tog PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tog 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=5tog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tog OCA], [~~http~~://pdbe.org/5tog PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tog RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tog PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tog 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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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Biel~~, J T~~]]	+	[[Category: Biel JT]]
-	[[Category: Corn~~, J E~~]]	+	[[Category: Corn JE]]
-	[[Category: Cunningham~~, C N~~]]	+	[[Category: Cunningham CN]]
-	[[Category: Fraser~~, J S~~]]	+	[[Category: Fraser JS]]
-	[[Category: Thompson~~, M C]]~~	+	[[Category: Thompson MC]]
-	~~[[Category: Computationally designed ubiquitin]]~~	+
-	~~[[Category: Signaling protein]]~~	+
-	~~[[Category: Usp7~~]]	+

OCA at 07:53, 27 November 2019

2019-11-27T07:53:34Z

←Older revision		Revision as of 07:53, 27 November 2019
Line 1:		Line 1:

	==Room temperature structure of ubiquitin variant u7ub25.2540==		==Room temperature structure of ubiquitin variant u7ub25.2540==
-	<StructureSection load='5tog' size='340' side='right' caption='[[5tog]], [[Resolution\|resolution]] 1.08Å' scene=''>	+	<StructureSection load='5tog' size='340' side='right'caption='[[5tog]], [[Resolution\|resolution]] 1.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5tog]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TOG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TOG FirstGlance]. <br>		<table><tr><td colspan='2'>[[5tog]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TOG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TOG FirstGlance]. <br>
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Biel, J T]]		[[Category: Biel, J T]]
	[[Category: Corn, J E]]		[[Category: Corn, J E]]

OCA at 14:26, 6 November 2017

2017-11-06T14:26:07Z

←Older revision		Revision as of 14:26, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5tog' size='340' side='right' caption='[[5tog]], [[Resolution\|resolution]] 1.08Å' scene=''>		<StructureSection load='5tog' size='340' side='right' caption='[[5tog]], [[Resolution\|resolution]] 1.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tog]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TOG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TOG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tog]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TOG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TOG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tof\|5tof]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tof\|5tof]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">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=5tog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tog OCA], [http://pdbe.org/5tog PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tog RCSB], [http://www.ebi.ac.uk/pdbsum/5tog PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tog 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=5tog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tog OCA], [http://pdbe.org/5tog PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tog RCSB], [http://www.ebi.ac.uk/pdbsum/5tog PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tog ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Biel, J T]]		[[Category: Biel, J T]]
	[[Category: Corn, J E]]		[[Category: Corn, J E]]

OCA at 13:37, 24 May 2017

2017-05-24T13:37:56Z

←Older revision		Revision as of 13:37, 24 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5tog is ~~ON HOLD~~	+	==Room temperature structure of ubiquitin variant u7ub25.2540==
		+	<StructureSection load='5tog' size='340' side='right' caption='[[5tog]], [[Resolution\|resolution]] 1.08Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5tog]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TOG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TOG FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tof\|5tof]]</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=5tog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tog OCA], [http://pdbe.org/5tog PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tog RCSB], [http://www.ebi.ac.uk/pdbsum/5tog PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tog 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 ==
		+	Although protein design has been used to introduce new functions, designed variants generally only function as well as natural proteins after rounds of laboratory evolution. One possibility for this pattern is that designed mutants frequently sample nonfunctional conformations. To test this idea, we exploited advances in multiconformer modeling of room-temperature X-ray data collection on redesigned ubiquitin variants selected for increasing binding affinity to the deubiquitinase USP7. Initial core mutations disrupt natural packing and lead to increased flexibility. Additional, experimentally selected mutations quenched conformational heterogeneity through new stabilizing interactions. Stabilizing interactions, such as cation-pi stacking and ordered waters, which are not included in standard protein design energy functions, can create specific interactions that have long-range effects on flexibility across the protein. Our results suggest that increasing flexibility may be a useful strategy to escape local minima during initial directed evolution and protein design steps when creating new functions.

-	~~Authors~~: ~~Biel, J.T~~., Thompson~~, M.C.~~, Cunningham~~, C.N.~~, Corn, J.E.~~, Fraser, J~~.S.	+	Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin.,Biel JT, Thompson MC, Cunningham CN, Corn JE, Fraser JS Structure. 2017 May 2;25(5):739-749.e3. doi: 10.1016/j.str.2017.03.009. Epub 2017, Apr 13. PMID:28416112<ref>PMID:28416112</ref>

-	~~Description: Room temperature structure~~ of ~~ubiquitin variant u7ub25~~.~~2540~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Biel~~, J.T]]	+	<div class="pdbe-citations 5tog" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Thompson~~, M.C]]	+	== References ==
-	[[Category: Fraser, J.S]]	+	<references/>
-	[[Category: ~~Cunningham~~, C.N]]	+	__TOC__
-	[[Category: ~~Corn, J.E~~]]	+	</StructureSection>
		+	[[Category: Biel, J T]]
		+	[[Category: Corn, J E]]
		+	[[Category: Cunningham, C N]]
		+	[[Category: Fraser, J S]]
		+	[[Category: Thompson, M C]]
		+	[[Category: Computationally designed ubiquitin]]
		+	[[Category: Signaling protein]]
		+	[[Category: Usp7]]

OCA at 13:40, 9 March 2017

2017-03-09T13:40:12Z

←Older revision		Revision as of 13:40, 9 March 2017
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	Description: Room temperature structure of ubiquitin variant u7ub25.2540		Description: Room temperature structure of ubiquitin variant u7ub25.2540
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Biel, J.T]]
	[[Category: Thompson, M.C]]		[[Category: Thompson, M.C]]
		+	[[Category: Fraser, J.S]]
	[[Category: Cunningham, C.N]]		[[Category: Cunningham, C.N]]
	[[Category: Corn, J.E]]		[[Category: Corn, J.E]]
-	[[Category: Biel, J.T]]
-	[[Category: Fraser, J.S]]

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

2016-10-26T17:18:23Z

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

←Older revision

Revision as of 17:18, 26 October 2016

OCA: New page: '''Unreleased structure''' The entry 5tog is ON HOLD Authors: Biel, J.T., Thompson, M.C., Cunningham, C.N., Corn, J.E., Fraser, J.S. Description: Room temperature structure of ubiquiti...

2016-10-26T17:18:22Z

New page: '''Unreleased structure''' The entry 5tog is ON HOLD Authors: Biel, J.T., Thompson, M.C., Cunningham, C.N., Corn, J.E., Fraser, J.S. Description: Room temperature structure of ubiquiti...

New page

'''Unreleased structure'''

The entry 5tog is ON HOLD

Authors: Biel, J.T., Thompson, M.C., Cunningham, C.N., Corn, J.E., Fraser, J.S.

Description: Room temperature structure of ubiquitin variant u7ub25.2540
[[Category: Unreleased Structures]]
[[Category: Thompson, M.C]]
[[Category: Cunningham, C.N]]
[[Category: Corn, J.E]]
[[Category: Biel, J.T]]
[[Category: Fraser, J.S]]