4xol - Revision history

OCA at 10:50, 10 January 2024

OCA — Wed, 10 Jan 2024 10:50:05 GMT

←Older revision		Revision as of 10:50, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xol]] is a 2 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=4XOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XOL FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xol]] is a 2 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=4XOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XOL FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.91Å</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=4xol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xol OCA], [https://pdbe.org/4xol PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xol RCSB], [https://www.ebi.ac.uk/pdbsum/4xol PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xol 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=4xol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xol OCA], [https://pdbe.org/4xol PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xol RCSB], [https://www.ebi.ac.uk/pdbsum/4xol PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xol ProSAT]</span></td></tr>
	</table>		</table>

OCA at 17:45, 26 April 2023

OCA — Wed, 26 Apr 2023 17:45:42 GMT

←Older revision		Revision as of 17:45, 26 April 2023
Line 3:		Line 3:
	<StructureSection load='4xol' size='340' side='right'caption='[[4xol]], [[Resolution\|resolution]] 2.91Å' scene=''>		<StructureSection load='4xol' size='340' side='right'caption='[[4xol]], [[Resolution\|resolution]] 2.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xol]] is a 2 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=4XOL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XOL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xol]] is a 2 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=4XOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XOL 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" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBC ([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=4xol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xol OCA], [https://pdbe.org/4xol PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xol RCSB], [https://www.ebi.ac.uk/pdbsum/4xol PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xol 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=4xol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xol OCA], [~~http~~://pdbe.org/4xol PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xol RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xol PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xol 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 21:		Line 20:

	==See Also==		==See Also==
-	*[[~~Ubiquitin~~\|~~Ubiquitin~~]]	+	*[[3D structures of ubiquitin\|3D structures of ubiquitin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Colletier~~, J P~~]]	+	[[Category: Colletier JP]]
-	[[Category: Coquelle, N]]	+	[[Category: Coquelle N]]
-	[[Category: Peixiang, M]]	+	[[Category: Peixiang M]]
-	[[Category: Schanda, P]]	+	[[Category: Schanda P]]
-	~~[[Category: Signaling protein~~]]	+

OCA at 00:07, 6 June 2019

OCA — Thu, 06 Jun 2019 00:07:34 GMT

←Older revision		Revision as of 00:07, 6 June 2019
Line 1:		Line 1:
		+
	==Observing the overall rocking motion of a protein in a crystal - Cubic Ubiquitin crystals.==		==Observing the overall rocking motion of a protein in a crystal - Cubic Ubiquitin crystals.==
-	<StructureSection load='4xol' size='340' side='right' caption='[[4xol]], [[Resolution\|resolution]] 2.91Å' scene=''>	+	<StructureSection load='4xol' size='340' side='right'caption='[[4xol]], [[Resolution\|resolution]] 2.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xol]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XOL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XOL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xol]] is a 2 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=4XOL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XOL 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='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=4xol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xol OCA], [http://pdbe.org/4xol PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xol RCSB], [http://www.ebi.ac.uk/pdbsum/4xol PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBC ([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=4xol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xol OCA], [http://pdbe.org/4xol PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xol RCSB], [http://www.ebi.ac.uk/pdbsum/4xol PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xol ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 4xol" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4xol" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ubiquitin\|Ubiquitin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Colletier, J P]]		[[Category: Colletier, J P]]
	[[Category: Coquelle, N]]		[[Category: Coquelle, N]]

OCA at 03:56, 16 October 2015

OCA — Fri, 16 Oct 2015 03:56:59 GMT

←Older revision		Revision as of 03:56, 16 October 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Observing the overall rocking motion of a protein in a crystal - Cubic Ubiquitin crystals.==
		+	<StructureSection load='4xol' size='340' side='right' caption='[[4xol]], [[Resolution\|resolution]] 2.91Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xol]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XOL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XOL 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='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=4xol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xol OCA], [http://pdbe.org/4xol PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xol RCSB], [http://www.ebi.ac.uk/pdbsum/4xol PDBsum]</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 ==
		+	The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall 'rocking' motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and mus-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1-100 mus. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments.

-	~~The entry 4xol is ON HOLD until Paper Publication~~	+	Observing the overall rocking motion of a protein in a crystal.,Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold D, Colletier JP, Skrynnikov NR, Schanda P Nat Commun. 2015 Oct 5;6:8361. doi: 10.1038/ncomms9361. PMID:26436197<ref>PMID:26436197</ref>

-	~~Authors: Coquelle~~, N.~~, Peixiang, M~~.~~, Schanda, P., Colletier, J.P~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Observing the overall rocking motion of a protein in a crystal -Cubic Ubiquitin crystals.~~	+	<div class="pdbe-citations 4xol" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Colletier, J P]]
	[[Category: Coquelle, N]]		[[Category: Coquelle, N]]
	[[Category: Peixiang, M]]		[[Category: Peixiang, M]]
-	[[Category: Colletier, J.P]]
	[[Category: Schanda, P]]		[[Category: Schanda, P]]
		+	[[Category: Signaling protein]]

OCA at 11:33, 17 June 2015

OCA — Wed, 17 Jun 2015 11:33:23 GMT

←Older revision		Revision as of 11:33, 17 June 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xol is ON HOLD	+	The entry 4xol is ON HOLD until Paper Publication

	Authors: Coquelle, N., Peixiang, M., Schanda, P., Colletier, J.P.		Authors: Coquelle, N., Peixiang, M., Schanda, P., Colletier, J.P.

OCA: Protected "4xol" [edit=sysop:move=sysop]

OCA — Wed, 28 Jan 2015 15:36:59 GMT

Protected "4xol" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:36, 28 January 2015

OCA: New page: '''Unreleased structure''' The entry 4xol is ON HOLD Authors: Coquelle, N., Peixiang, M., Schanda, P., Colletier, J.P. Description: Observing the overall rocking motion of a protein in...

OCA — Wed, 28 Jan 2015 15:36:58 GMT

New page: '''Unreleased structure''' The entry 4xol is ON HOLD Authors: Coquelle, N., Peixiang, M., Schanda, P., Colletier, J.P. Description: Observing the overall rocking motion of a protein in...

New page

'''Unreleased structure'''

The entry 4xol is ON HOLD

Authors: Coquelle, N., Peixiang, M., Schanda, P., Colletier, J.P.

Description: Observing the overall rocking motion of a protein in a crystal -Cubic Ubiquitin crystals.
[[Category: Unreleased Structures]]
[[Category: Coquelle, N]]
[[Category: Peixiang, M]]
[[Category: Colletier, J.P]]
[[Category: Schanda, P]]