7cap - Revision history

OCA at 09:22, 9 October 2024

2024-10-09T09:22:08Z

← Older revision		Revision as of 09:22, 9 October 2024
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	<StructureSection load='7cap' size='340' side='right'caption='[[7cap]], [[Resolution\|resolution]] 1.33Å' scene=''>		<StructureSection load='7cap' size='340' side='right'caption='[[7cap]], [[Resolution\|resolution]] 1.33Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[7cap]] is a 3 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=7CAP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CAP FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CAP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CAP FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.33Å</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]] 1.33Å</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='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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7cap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cap OCA], [https://pdbe.org/7cap PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cap RCSB], [https://www.ebi.ac.uk/pdbsum/7cap PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cap 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=7cap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cap OCA], [https://pdbe.org/7cap PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cap RCSB], [https://www.ebi.ac.uk/pdbsum/7cap PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cap ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	[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: Homo sapiens]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Hiranyakorn M]]		[[Category: Hiranyakorn M]]

OCA at 16:01, 29 November 2023

2023-11-29T16:01:16Z

← Older revision		Revision as of 16:01, 29 November 2023
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	==Cyclic Lys48-linked triubiquitin==		==Cyclic Lys48-linked triubiquitin==
	<StructureSection load='7cap' size='340' side='right'caption='[[7cap]]' scene=''>		<StructureSection load='7cap' size='340' side='right'caption='[[7cap]], [[Resolution\|resolution]] 1.33Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CAP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CAP FirstGlance]. <br>		<table><tr><td colspan='2'>[[7cap]] is a 3 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=7CAP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CAP FirstGlance]. <br>
	</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=7cap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cap OCA], [https://pdbe.org/7cap PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cap RCSB], [https://www.ebi.ac.uk/pdbsum/7cap PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cap 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]] 1.33Å</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7cap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cap OCA], [https://pdbe.org/7cap PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cap RCSB], [https://www.ebi.ac.uk/pdbsum/7cap PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cap ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[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;">
			== Publication Abstract from PubMed ==
			Ubiquitin (Ub) molecules can be enzymatically connected through a specific isopeptide linkage, thereby mediating various cellular processes by binding to Ub-interacting proteins through their hydrophobic surfaces. The Lys48-linked Ub chains, which serve as tags for proteasomal degradation, undergo conformational interconversions between open and closed states, in which the hydrophobic surfaces are exposed and shielded, respectively. Here, we provide a quantitative view of such dynamic processes of Lys48-linked triUb and tetraUb in solution. The native and cyclic forms of Ub chains are prepared with isotope labeling by in vitro enzymatic reactions. Our comparative NMR analyses using monomeric Ub and cyclic diUb as reference molecules enabled the quantification of populations of the open and closed states for each Ub unit of the native Ub chains. The data indicate that the most distal Ub unit in the Ub chains is the most apt to expose its hydrophobic surface, suggesting its preferential involvement in interactions with the Ub-recognizing proteins. We also demonstrate that a mutational modification of the distal end of the Ub chain can remotely affect the solvent exposure of the hydrophobic surfaces of the other Ub units, suggesting that Ub chains could be unique design frameworks for the creation of allosterically controllable multidomain proteins.

			NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin Chains.,Hiranyakorn M, Yanaka S, Satoh T, Wilasri T, Jityuti B, Yagi-Utsumi M, Kato K Int J Mol Sci. 2020 Jul 28;21(15). pii: ijms21155351. doi: 10.3390/ijms21155351. PMID:32731397<ref>PMID:32731397</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7cap" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[3D structures of ubiquitin\|3D structures of ubiquitin]]		*[[3D structures of ubiquitin\|3D structures of ubiquitin]]
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Hiranyakorn M]]		[[Category: Hiranyakorn M]]

OCA at 06:17, 24 December 2021

2021-12-24T06:17:20Z

← Older revision		Revision as of 06:17, 24 December 2021
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	<StructureSection load='7cap' size='340' side='right'caption='[[7cap]]' scene=''>		<StructureSection load='7cap' size='340' side='right'caption='[[7cap]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CAP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7CAP FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CAP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CAP FirstGlance]. <br>
	</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=7cap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cap OCA], [~~http~~://pdbe.org/7cap PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7cap RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7cap PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7cap ProSAT]</span></td></tr>		</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=7cap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cap OCA], [https://pdbe.org/7cap PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cap RCSB], [https://www.ebi.ac.uk/pdbsum/7cap PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cap ProSAT]</span></td></tr>
	</table>		</table>

			==See Also==
			*[[3D structures of ubiquitin\|3D structures of ubiquitin]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:24, 19 August 2020

2020-08-19T06:24:53Z

← Older revision		Revision as of 06:24, 19 August 2020
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	~~'''Unreleased structure'''~~

	~~The entry~~ 7cap is ~~ON HOLD until Paper Publication~~		==Cyclic Lys48-linked triubiquitin==
			<StructureSection load='7cap' size='340' side='right'caption='[[7cap]]' scene=''>
	~~Authors~~:		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CAP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7CAP FirstGlance]. <br>
	~~Description~~:		</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=7cap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cap OCA], [http://pdbe.org/7cap PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7cap RCSB], [http://www.ebi.ac.uk/pdbsum/7cap PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7cap ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Hiranyakorn M]]
			[[Category: Jityuti B]]
			[[Category: Kato K]]
			[[Category: Satoh T]]
			[[Category: Wilasri T]]
			[[Category: Yagi-Utsumi T]]
			[[Category: Yanaka S]]

OCA at 18:51, 24 June 2020

2020-06-24T18:51:03Z

← Older revision		Revision as of 18:51, 24 June 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7cap is ON HOLD		The entry 7cap is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7cap" [edit=sysop:move=sysop]

2020-06-17T09:02:35Z

Protected "7cap" [edit=sysop:move=sysop]

← Older revision	Revision as of 09:02, 17 June 2020
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7cap is ON HOLD Authors: Description: Category: Unreleased Structures

2020-06-17T09:02:33Z

New page: '''Unreleased structure''' The entry 7cap is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7cap is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]