2lj5 - Revision history

OCA at 06:55, 1 May 2024

OCA — Wed, 01 May 2024 06:55:52 GMT

←Older revision		Revision as of 06:55, 1 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2lj5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LJ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LJ5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2lj5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LJ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LJ5 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=2lj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lj5 OCA], [https://pdbe.org/2lj5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lj5 RCSB], [https://www.ebi.ac.uk/pdbsum/2lj5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lj5 ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2lj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lj5 OCA], [https://pdbe.org/2lj5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lj5 RCSB], [https://www.ebi.ac.uk/pdbsum/2lj5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lj5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/RL40_HUMAN RL40_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> Ribosomal protein L40 is a component of the 60S subunit of the ribosome.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>		[https://www.uniprot.org/uniprot/RL40_HUMAN RL40_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> Ribosomal protein L40 is a component of the 60S subunit of the ribosome.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Residual dipolar couplings (RDCs) have the potential of providing detailed information about the conformational fluctuations of proteins. It is very challenging, however, to extract such information because of the complex relationship between RDCs and protein structures. A promising approach to decode this relationship involves structure-based calculations of the alignment tensors of protein conformations. By implementing this strategy to generate structural restraints in molecular dynamics simulations we show that it is possible to extract effectively the information provided by RDCs about the conformational fluctuations in the native states of proteins. The approach that we present can be used in a wide range of alignment media, including Pf1, charged bicelles and gels. The accuracy of the method is demonstrated by the analysis of the Q factors for RDCs not used as restraints in the calculations, which are significantly lower than those corresponding to existing high-resolution structures and structural ensembles, hence showing that we capture effectively the contributions to RDCs from conformational fluctuations.
-
-	Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings.,Montalvao RW, De Simone A, Vendruscolo M J Biomol NMR. 2012 Jun 23. PMID:22729708<ref>PMID:22729708</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2lj5" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:02, 15 February 2023

OCA — Wed, 15 Feb 2023 11:02:23 GMT

←Older revision		Revision as of 11:02, 15 February 2023
Line 1:		Line 1:

	==Description of the Structural fluctuations of proteins from structure-based calculations of Residual dipolar couplings==		==Description of the Structural fluctuations of proteins from structure-based calculations of Residual dipolar couplings==
-	<StructureSection load='2lj5' size='340' side='right'caption='[[2lj5~~]], [[NMR_Ensembles_of_Models \| 301 NMR models~~]]' scene=''>	+	<StructureSection load='2lj5' size='340' side='right'caption='[[2lj5]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2lj5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LJ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LJ5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2lj5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LJ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LJ5 FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2kox\|2kox]]</div></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=2lj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lj5 OCA], [https://pdbe.org/2lj5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lj5 RCSB], [https://www.ebi.ac.uk/pdbsum/2lj5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lj5 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBA52, UBCEP2, RPS27A, UBA80, UBCEP1, UBB, UBC ([https://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=2lj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lj5 OCA], [https://pdbe.org/2lj5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lj5 RCSB], [https://www.ebi.ac.uk/pdbsum/2lj5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lj5 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RL40_HUMAN RL40_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> Ribosomal protein L40 is a component of the 60S subunit of the ribosome.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>	+	[https://www.uniprot.org/uniprot/RL40_HUMAN RL40_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> Ribosomal protein L40 is a component of the 60S subunit of the ribosome.<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 23:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Montalvao, R~~]]	+	[[Category: De Simone A]]
-	[[Category: ~~Simone, A De~~]]	+	[[Category: Montalvao R]]
-	[[Category: Vendruscolo, M]]	+	[[Category: Vendruscolo M]]
-	~~[[Category: Signaling protein~~]]	+

OCA at 10:11, 12 May 2021

OCA — Wed, 12 May 2021 10:11:38 GMT

←Older revision		Revision as of 10:11, 12 May 2021
Line 1:		Line 1:
-	~~{{Large structure}}~~	+
	==Description of the Structural fluctuations of proteins from structure-based calculations of Residual dipolar couplings==		==Description of the Structural fluctuations of proteins from structure-based calculations of Residual dipolar couplings==
-	<StructureSection load='2lj5' size='340' side='right' caption='[[2lj5]], [[NMR_Ensembles_of_Models \| 301 NMR models]]' scene=''>	+	<StructureSection load='2lj5' size='340' side='right'caption='[[2lj5]], [[NMR_Ensembles_of_Models \| 301 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2lj5]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LJ5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2LJ5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2lj5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LJ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LJ5 FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2kox\|2kox]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2kox\|2kox]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBA52, UBCEP2, RPS27A, UBA80, UBCEP1, UBB, UBC ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBA52, UBCEP2, RPS27A, UBA80, UBCEP1, UBB, UBC ([https://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=2lj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lj5 OCA], [~~http~~://pdbe.org/2lj5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2lj5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2lj5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2lj5 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=2lj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lj5 OCA], [https://pdbe.org/2lj5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lj5 RCSB], [https://www.ebi.ac.uk/pdbsum/2lj5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lj5 ProSAT]</span></td></tr>
	</table>		</table>
-	{{Large structure}}
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RL40_HUMAN RL40_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> Ribosomal protein L40 is a component of the 60S subunit of the ribosome.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>	+	[[https://www.uniprot.org/uniprot/RL40_HUMAN RL40_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> Ribosomal protein L40 is a component of the 60S subunit of the ribosome.<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 25:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Montalvao, R]]		[[Category: Montalvao, R]]
	[[Category: Simone, A De]]		[[Category: Simone, A De]]
	[[Category: Vendruscolo, M]]		[[Category: Vendruscolo, M]]
	[[Category: Signaling protein]]		[[Category: Signaling protein]]

OCA at 19:18, 1 August 2018

OCA — Wed, 01 Aug 2018 19:18:51 GMT

←Older revision		Revision as of 19:18, 1 August 2018
Line 1:		Line 1:
		+	{{Large structure}}
	==Description of the Structural fluctuations of proteins from structure-based calculations of Residual dipolar couplings==		==Description of the Structural fluctuations of proteins from structure-based calculations of Residual dipolar couplings==
	<StructureSection load='2lj5' size='340' side='right' caption='[[2lj5]], [[NMR_Ensembles_of_Models \| 301 NMR models]]' scene=''>		<StructureSection load='2lj5' size='340' side='right' caption='[[2lj5]], [[NMR_Ensembles_of_Models \| 301 NMR models]]' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2kox\|2kox]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2kox\|2kox]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBA52, UBCEP2, RPS27A, UBA80, UBCEP1, UBB, UBC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBA52, UBCEP2, RPS27A, UBA80, UBCEP1, UBB, 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=2lj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lj5 OCA], [http://pdbe.org/2lj5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lj5 RCSB], [http://www.ebi.ac.uk/pdbsum/2lj5 PDBsum]</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=2lj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lj5 OCA], [http://pdbe.org/2lj5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lj5 RCSB], [http://www.ebi.ac.uk/pdbsum/2lj5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2lj5 ProSAT]</span></td></tr>
	</table>		</table>
	{{Large structure}}		{{Large structure}}

OCA at 01:14, 12 September 2015

OCA — Sat, 12 Sep 2015 01:14:48 GMT

←Older revision		Revision as of 01:14, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='2lj5' size='340' side='right' caption='[[2lj5]], [[NMR_Ensembles_of_Models \| 301 NMR models]]' scene=''>		<StructureSection load='2lj5' size='340' side='right' caption='[[2lj5]], [[NMR_Ensembles_of_Models \| 301 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2lj5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LJ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LJ5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2lj5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LJ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LJ5 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2kox\|2kox]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2kox\|2kox]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBA52, UBCEP2, RPS27A, UBA80, UBCEP1, UBB, UBC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBA52, UBCEP2, RPS27A, UBA80, UBCEP1, UBB, 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=2lj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lj5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lj5 RCSB], [http://www.ebi.ac.uk/pdbsum/2lj5 PDBsum]</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=2lj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lj5 OCA], [http://pdbe.org/2lj5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lj5 RCSB], [http://www.ebi.ac.uk/pdbsum/2lj5 PDBsum]</span></td></tr>
	</table>		</table>
		+	{{Large structure}}
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RL40_HUMAN RL40_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> Ribosomal protein L40 is a component of the 60S subunit of the ribosome.<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 15:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2lj5" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Montalvao, R]]		[[Category: Montalvao, R]]
	[[Category: Simone, A De]]		[[Category: Simone, A De]]
	[[Category: Vendruscolo, M]]		[[Category: Vendruscolo, M]]
	[[Category: Signaling protein]]		[[Category: Signaling protein]]

OCA at 13:45, 17 December 2014

OCA — Wed, 17 Dec 2014 13:45:56 GMT

←Older revision		Revision as of 13:45, 17 December 2014
Line 1:		Line 1:
-	~~{{Large structure}}~~	+	==Description of the Structural fluctuations of proteins from structure-based calculations of Residual dipolar couplings==
-	~~{{STRUCTURE_2lj5\| PDB=2lj5 \| SCENE= }}~~	+	<StructureSection load='2lj5' size='340' side='right' caption='[[2lj5]], [[NMR_Ensembles_of_Models \| 301 NMR models]]' scene=''>
-	===Description of the Structural fluctuations of proteins from structure-based calculations of Residual dipolar couplings===	+	== Structural highlights ==
-	~~{{ABSTRACT_PUBMED_22729708}}~~	+	<table><tr><td colspan='2'>[[2lj5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LJ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LJ5 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2kox\|2kox]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBA52, UBCEP2, RPS27A, UBA80, UBCEP1, UBB, UBC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=2lj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lj5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lj5 RCSB], [http://www.ebi.ac.uk/pdbsum/2lj5 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Residual dipolar couplings (RDCs) have the potential of providing detailed information about the conformational fluctuations of proteins. It is very challenging, however, to extract such information because of the complex relationship between RDCs and protein structures. A promising approach to decode this relationship involves structure-based calculations of the alignment tensors of protein conformations. By implementing this strategy to generate structural restraints in molecular dynamics simulations we show that it is possible to extract effectively the information provided by RDCs about the conformational fluctuations in the native states of proteins. The approach that we present can be used in a wide range of alignment media, including Pf1, charged bicelles and gels. The accuracy of the method is demonstrated by the analysis of the Q factors for RDCs not used as restraints in the calculations, which are significantly lower than those corresponding to existing high-resolution structures and structural ensembles, hence showing that we capture effectively the contributions to RDCs from conformational fluctuations.

-	~~==About this Structure==~~	+	Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings.,Montalvao RW, De Simone A, Vendruscolo M J Biomol NMR. 2012 Jun 23. PMID:22729708<ref>PMID:22729708</ref>
-	~~[[2lj5]] is a 1 chain~~ structure ~~with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full experimental information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2LJ5 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	<~~ref group="xtra">PMID:022729708<~~/~~ref~~><~~references group="xtra"~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Montalvao, R.]]	+	[[Category: Montalvao, R]]
-	[[Category: Simone, A De.]]	+	[[Category: Simone, A De]]
-	[[Category: Vendruscolo, M.]]	+	[[Category: Vendruscolo, M]]
	[[Category: Signaling protein]]		[[Category: Signaling protein]]

OCA at 07:37, 11 March 2013

OCA — Mon, 11 Mar 2013 07:37:45 GMT

←Older revision		Revision as of 07:37, 11 March 2013
Line 1:		Line 1:
	{{Large structure}}		{{Large structure}}
-	[[Image:2lj5.png\|left\|200px]]
-
	{{STRUCTURE_2lj5\| PDB=2lj5 \| SCENE= }}		{{STRUCTURE_2lj5\| PDB=2lj5 \| SCENE= }}
-
	===Description of the Structural fluctuations of proteins from structure-based calculations of Residual dipolar couplings===		===Description of the Structural fluctuations of proteins from structure-based calculations of Residual dipolar couplings===
-
	{{ABSTRACT_PUBMED_22729708}}		{{ABSTRACT_PUBMED_22729708}}

OCA at 04:29, 8 August 2012

OCA — Wed, 08 Aug 2012 04:29:06 GMT

←Older revision		Revision as of 04:29, 8 August 2012
Line 1:		Line 1:
	{{Large structure}}		{{Large structure}}
-	[[Image:2lj5.~~jpg~~\|left\|200px]]	+	[[Image:2lj5.png\|left\|200px]]

	{{STRUCTURE_2lj5\| PDB=2lj5 \| SCENE= }}		{{STRUCTURE_2lj5\| PDB=2lj5 \| SCENE= }}

OCA at 05:21, 18 July 2012

OCA — Wed, 18 Jul 2012 05:21:54 GMT

←Older revision		Revision as of 05:21, 18 July 2012
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{Large structure}}
		+	[[Image:2lj5.jpg\|left\|200px]]

-	~~The entry~~ 2lj5 ~~is ON HOLD~~	+	{{STRUCTURE_2lj5\| PDB=2lj5 \| SCENE= }}

-	~~Authors: De Simone, A., Montalvao, R., Vendruscolo, M.~~	+	===Description of the Structural fluctuations of proteins from structure-based calculations of Residual dipolar couplings===

-	~~Description~~: ~~Description of the Structural fluctuations of proteins~~ from ~~structure~~-~~based calculations of Residual dipolar couplings~~	+	{{ABSTRACT_PUBMED_22729708}}
		+
		+	==About this Structure==
		+	[[2lj5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LJ5 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022729708</ref><references group="xtra"/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Montalvao, R.]]
		+	[[Category: Simone, A De.]]
		+	[[Category: Vendruscolo, M.]]
		+	[[Category: Signaling protein]]

OCA at 07:11, 22 February 2012

OCA — Wed, 22 Feb 2012 07:11:48 GMT

←Older revision		Revision as of 07:11, 22 February 2012
Line 5:		Line 5:
	Authors: De Simone, A., Montalvao, R., Vendruscolo, M.		Authors: De Simone, A., Montalvao, R., Vendruscolo, M.

-	Description: 'Description of the ~~structural~~ fluctuations of proteins from structure-based calculations of ~~residual~~ dipolar couplings	+	Description: Description of the Structural fluctuations of proteins from structure-based calculations of Residual dipolar couplings