3qxy - Revision history

OCA at 10:50, 21 February 2024

OCA — Wed, 21 Feb 2024 10:50:40 GMT

←Older revision		Revision as of 10:50, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3qxy' size='340' side='right'caption='[[3qxy]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='3qxy' size='340' side='right'caption='[[3qxy]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qxy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QXY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qxy]] is a 4 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=3QXY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QXY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1~~,2~~-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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]] 2.09Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~SETD6 ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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=3qxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxy OCA], [https://pdbe.org/3qxy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qxy RCSB], [https://www.ebi.ac.uk/pdbsum/3qxy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxy 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=3qxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxy OCA], [https://pdbe.org/3qxy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qxy RCSB], [https://www.ebi.ac.uk/pdbsum/3qxy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SETD6_HUMAN SETD6_HUMAN]] Protein-lysine N-methyltransferase that specifically monomethylates 'Lys-310' of the RELA subunit of NF-kappa-B complex, leading to down-regulate NF-kappa-B transcription factor activity.<ref>PMID:21131967</ref> [[https://www.uniprot.org/uniprot/TF65_HUMAN TF65_HUMAN]] NF-kappa-B is a pleiotropic transcription factor present in almost all cell types and is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. NF-kappa-B is a homo- or heterodimeric complex formed by the Rel-like domain-containing proteins RELA/p65, RELB, NFKB1/p105, NFKB1/p50, REL and NFKB2/p52 and the heterodimeric p65-p50 complex appears to be most abundant one. The dimers bind at kappa-B sites in the DNA of their target genes and the individual dimers have distinct preferences for different kappa-B sites that they can bind with distinguishable affinity and specificity. Different dimer combinations act as transcriptional activators or repressors, respectively. NF-kappa-B is controlled by various mechanisms of post-translational modification and subcellular compartmentalization as well as by interactions with other cofactors or corepressors. NF-kappa-B complexes are held in the cytoplasm in an inactive state complexed with members of the NF-kappa-B inhibitor (I-kappa-B) family. In a conventional activation pathway, I-kappa-B is phosphorylated by I-kappa-B kinases (IKKs) in response to different activators, subsequently degraded thus liberating the active NF-kappa-B complex which translocates to the nucleus. NF-kappa-B heterodimeric p65-p50 and p65-c-Rel complexes are transcriptional activators. The NF-kappa-B p65-p65 complex appears to be involved in invasin-mediated activation of IL-8 expression. The inhibitory effect of I-kappa-B upon NF-kappa-B the cytoplasm is exerted primarily through the interaction with p65. p65 shows a weak DNA-binding site which could contribute directly to DNA binding in the NF-kappa-B complex. Associates with chromatin at the NF-kappa-B promoter region via association with DDX1.<ref>PMID:10928981</ref> <ref>PMID:12748188</ref> <ref>PMID:17000776</ref> <ref>PMID:17620405</ref> <ref>PMID:19058135</ref> <ref>PMID:20547752</ref>	+	[https://www.uniprot.org/uniprot/SETD6_HUMAN SETD6_HUMAN] Protein-lysine N-methyltransferase that specifically monomethylates 'Lys-310' of the RELA subunit of NF-kappa-B complex, leading to down-regulate NF-kappa-B transcription factor activity.<ref>PMID:21131967</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	SET domain containing 6 (SETD6) monomethylates the RelA subunit of nuclear factor kappa B (NF-kappaB). The ankyrin repeats of G9a-like protein (GLP) recognizes RelA monomethylated at Lys310. Adjacent to Lys310 is Ser311, a known phosphorylation site of RelA. Ser311 phosphorylation inhibits Lys310 methylation by SETD6 as well as binding of Lys310me1 by GLP. The structure of SETD6 in complex with RelA peptide containing the methylation site, in the presence of S-adenosyl-l-methionine, reveals a V-like protein structure and suggests a model for NF-kappaB binding to SETD6. In addition, structural modeling of the GLP ankyrin repeats bound to Lys310me1 peptide provides insight into the molecular basis for inhibition of Lys310me1 binding by Ser311 phosphorylation. Together, these findings provide a structural explanation for a key cellular signaling pathway centered on RelA Lys310 methylation, which is generated by SETD6 and recognized by GLP, and incorporate a methylation-phosphorylation switch of adjacent lysine and serine residues. Finally, SETD6 is structurally similar to the Rubisco large subunit methyltransferase. Given the restriction of Rubisco to plant species, this particular appearance of the protein lysine methyltransferase has been evolutionarily well conserved.	+
-		+
-	Structural basis of SETD6-mediated regulation of the NF-kB network via methyl-lysine signaling.,Chang Y, Levy D, Horton JR, Peng J, Zhang X, Gozani O, Cheng X Nucleic Acids Res. 2011 Apr 22. PMID:21515635<ref>PMID:21515635</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3qxy" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 26:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chang, Y]]	+	[[Category: Chang Y]]
-	[[Category: Cheng, X]]	+	[[Category: Cheng X]]
-	[[Category: Gozani, O]]	+	[[Category: Gozani O]]
-	[[Category: Horton~~, J R~~]]	+	[[Category: Horton JR]]
-	[[Category: Levy, D]]	+	[[Category: Levy D]]
-	[[Category: Peng, J]]	+	[[Category: Peng J]]
-	[[Category: Zhang, X]]	+	[[Category: Zhang X]]
-	~~[[Category: Epigenetic]]~~	+
-	~~[[Category: Nf-kb network via methyllysine signaling]]~~	+
-	~~[[Category: Protein lysine methyltransferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 05:40, 15 June 2022

OCA — Wed, 15 Jun 2022 05:40:52 GMT

←Older revision		Revision as of 05:40, 15 June 2022
Line 1:		Line 1:

	==Human SETD6 in complex with RelA Lys310==		==Human SETD6 in complex with RelA Lys310==
-	<StructureSection load='3qxy' size='340' side='right' caption='[[3qxy]], [[Resolution\|resolution]] 2.09Å' scene=''>	+	<StructureSection load='3qxy' size='340' side='right'caption='[[3qxy]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qxy]] is a 4 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=3QXY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3QXY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qxy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QXY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SETD6 ([~~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">SETD6 ([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=3qxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxy OCA], [~~http~~://pdbe.org/3qxy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3qxy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3qxy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxy 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=3qxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxy OCA], [https://pdbe.org/3qxy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qxy RCSB], [https://www.ebi.ac.uk/pdbsum/3qxy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SETD6_HUMAN SETD6_HUMAN]] Protein-lysine N-methyltransferase that specifically monomethylates 'Lys-310' of the RELA subunit of NF-kappa-B complex, leading to down-regulate NF-kappa-B transcription factor activity.<ref>PMID:21131967</ref> [[~~http~~://www.uniprot.org/uniprot/TF65_HUMAN TF65_HUMAN]] NF-kappa-B is a pleiotropic transcription factor present in almost all cell types and is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. NF-kappa-B is a homo- or heterodimeric complex formed by the Rel-like domain-containing proteins RELA/p65, RELB, NFKB1/p105, NFKB1/p50, REL and NFKB2/p52 and the heterodimeric p65-p50 complex appears to be most abundant one. The dimers bind at kappa-B sites in the DNA of their target genes and the individual dimers have distinct preferences for different kappa-B sites that they can bind with distinguishable affinity and specificity. Different dimer combinations act as transcriptional activators or repressors, respectively. NF-kappa-B is controlled by various mechanisms of post-translational modification and subcellular compartmentalization as well as by interactions with other cofactors or corepressors. NF-kappa-B complexes are held in the cytoplasm in an inactive state complexed with members of the NF-kappa-B inhibitor (I-kappa-B) family. In a conventional activation pathway, I-kappa-B is phosphorylated by I-kappa-B kinases (IKKs) in response to different activators, subsequently degraded thus liberating the active NF-kappa-B complex which translocates to the nucleus. NF-kappa-B heterodimeric p65-p50 and p65-c-Rel complexes are transcriptional activators. The NF-kappa-B p65-p65 complex appears to be involved in invasin-mediated activation of IL-8 expression. The inhibitory effect of I-kappa-B upon NF-kappa-B the cytoplasm is exerted primarily through the interaction with p65. p65 shows a weak DNA-binding site which could contribute directly to DNA binding in the NF-kappa-B complex. Associates with chromatin at the NF-kappa-B promoter region via association with DDX1.<ref>PMID:10928981</ref> <ref>PMID:12748188</ref> <ref>PMID:17000776</ref> <ref>PMID:17620405</ref> <ref>PMID:19058135</ref> <ref>PMID:20547752</ref>	+	[[https://www.uniprot.org/uniprot/SETD6_HUMAN SETD6_HUMAN]] Protein-lysine N-methyltransferase that specifically monomethylates 'Lys-310' of the RELA subunit of NF-kappa-B complex, leading to down-regulate NF-kappa-B transcription factor activity.<ref>PMID:21131967</ref> [[https://www.uniprot.org/uniprot/TF65_HUMAN TF65_HUMAN]] NF-kappa-B is a pleiotropic transcription factor present in almost all cell types and is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. NF-kappa-B is a homo- or heterodimeric complex formed by the Rel-like domain-containing proteins RELA/p65, RELB, NFKB1/p105, NFKB1/p50, REL and NFKB2/p52 and the heterodimeric p65-p50 complex appears to be most abundant one. The dimers bind at kappa-B sites in the DNA of their target genes and the individual dimers have distinct preferences for different kappa-B sites that they can bind with distinguishable affinity and specificity. Different dimer combinations act as transcriptional activators or repressors, respectively. NF-kappa-B is controlled by various mechanisms of post-translational modification and subcellular compartmentalization as well as by interactions with other cofactors or corepressors. NF-kappa-B complexes are held in the cytoplasm in an inactive state complexed with members of the NF-kappa-B inhibitor (I-kappa-B) family. In a conventional activation pathway, I-kappa-B is phosphorylated by I-kappa-B kinases (IKKs) in response to different activators, subsequently degraded thus liberating the active NF-kappa-B complex which translocates to the nucleus. NF-kappa-B heterodimeric p65-p50 and p65-c-Rel complexes are transcriptional activators. The NF-kappa-B p65-p65 complex appears to be involved in invasin-mediated activation of IL-8 expression. The inhibitory effect of I-kappa-B upon NF-kappa-B the cytoplasm is exerted primarily through the interaction with p65. p65 shows a weak DNA-binding site which could contribute directly to DNA binding in the NF-kappa-B complex. Associates with chromatin at the NF-kappa-B promoter region via association with DDX1.<ref>PMID:10928981</ref> <ref>PMID:12748188</ref> <ref>PMID:17000776</ref> <ref>PMID:17620405</ref> <ref>PMID:19058135</ref> <ref>PMID:20547752</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:

	==See Also==		==See Also==
-	*[[Histone methyltransferase\|Histone methyltransferase]]	+	*[[Histone methyltransferase 3D structures\|Histone methyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Chang, Y]]		[[Category: Chang, Y]]
	[[Category: Cheng, X]]		[[Category: Cheng, X]]

OCA at 12:09, 5 August 2016

OCA — Fri, 05 Aug 2016 12:09:44 GMT

←Older revision		Revision as of 12:09, 5 August 2016
Line 1:		Line 1:
		+
	==Human SETD6 in complex with RelA Lys310==		==Human SETD6 in complex with RelA Lys310==
	<StructureSection load='3qxy' size='340' side='right' caption='[[3qxy]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='3qxy' size='340' side='right' caption='[[3qxy]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qxy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qxy]] is a 4 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=3QXY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SETD6 ([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">SETD6 ([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=3qxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qxy RCSB], [http://www.ebi.ac.uk/pdbsum/3qxy 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=3qxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxy OCA], [http://pdbe.org/3qxy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qxy RCSB], [http://www.ebi.ac.uk/pdbsum/3qxy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/TF65_HUMAN TF65_HUMAN]] NF-kappa-B is a pleiotropic transcription factor present in almost all cell types and is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. NF-kappa-B is a homo- or heterodimeric complex formed by the Rel-like domain-containing proteins RELA/p65, RELB, NFKB1/p105, NFKB1/p50, REL and NFKB2/p52 and the heterodimeric p65-p50 complex appears to be most abundant one. The dimers bind at kappa-B sites in the DNA of their target genes and the individual dimers have distinct preferences for different kappa-B sites that they can bind with distinguishable affinity and specificity. Different dimer combinations act as transcriptional activators or repressors, respectively. NF-kappa-B is controlled by various mechanisms of post-translational modification and subcellular compartmentalization as well as by interactions with other cofactors or corepressors. NF-kappa-B complexes are held in the cytoplasm in an inactive state complexed with members of the NF-kappa-B inhibitor (I-kappa-B) family. In a conventional activation pathway, I-kappa-B is phosphorylated by I-kappa-B kinases (IKKs) in response to different activators, subsequently degraded thus liberating the active NF-kappa-B complex which translocates to the nucleus. NF-kappa-B heterodimeric p65-p50 and p65-c-Rel complexes are transcriptional activators. The NF-kappa-B p65-p65 complex appears to be involved in invasin-mediated activation of IL-8 expression. The inhibitory effect of I-kappa-B upon NF-kappa-B the cytoplasm is exerted primarily through the interaction with p65. p65 shows a weak DNA-binding site which could contribute directly to DNA binding in the NF-kappa-B complex. Associates with chromatin at the NF-kappa-B promoter region via association with DDX1.<ref>PMID:10928981</ref> <ref>PMID:12748188</ref> <ref>PMID:17000776</ref> <ref>PMID:17620405</ref> <ref>PMID:19058135</ref> <ref>PMID:20547752</ref>	+	[[http://www.uniprot.org/uniprot/SETD6_HUMAN SETD6_HUMAN]] Protein-lysine N-methyltransferase that specifically monomethylates 'Lys-310' of the RELA subunit of NF-kappa-B complex, leading to down-regulate NF-kappa-B transcription factor activity.<ref>PMID:21131967</ref> [[http://www.uniprot.org/uniprot/TF65_HUMAN TF65_HUMAN]] NF-kappa-B is a pleiotropic transcription factor present in almost all cell types and is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. NF-kappa-B is a homo- or heterodimeric complex formed by the Rel-like domain-containing proteins RELA/p65, RELB, NFKB1/p105, NFKB1/p50, REL and NFKB2/p52 and the heterodimeric p65-p50 complex appears to be most abundant one. The dimers bind at kappa-B sites in the DNA of their target genes and the individual dimers have distinct preferences for different kappa-B sites that they can bind with distinguishable affinity and specificity. Different dimer combinations act as transcriptional activators or repressors, respectively. NF-kappa-B is controlled by various mechanisms of post-translational modification and subcellular compartmentalization as well as by interactions with other cofactors or corepressors. NF-kappa-B complexes are held in the cytoplasm in an inactive state complexed with members of the NF-kappa-B inhibitor (I-kappa-B) family. In a conventional activation pathway, I-kappa-B is phosphorylated by I-kappa-B kinases (IKKs) in response to different activators, subsequently degraded thus liberating the active NF-kappa-B complex which translocates to the nucleus. NF-kappa-B heterodimeric p65-p50 and p65-c-Rel complexes are transcriptional activators. The NF-kappa-B p65-p65 complex appears to be involved in invasin-mediated activation of IL-8 expression. The inhibitory effect of I-kappa-B upon NF-kappa-B the cytoplasm is exerted primarily through the interaction with p65. p65 shows a weak DNA-binding site which could contribute directly to DNA binding in the NF-kappa-B complex. Associates with chromatin at the NF-kappa-B promoter region via association with DDX1.<ref>PMID:10928981</ref> <ref>PMID:12748188</ref> <ref>PMID:17000776</ref> <ref>PMID:17620405</ref> <ref>PMID:19058135</ref> <ref>PMID:20547752</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		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 3qxy" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 24:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Chang, Y]]		[[Category: Chang, Y]]
	[[Category: Cheng, X]]		[[Category: Cheng, X]]

OCA at 18:43, 25 December 2014

OCA — Thu, 25 Dec 2014 18:43:05 GMT

←Older revision		Revision as of 18:43, 25 December 2014
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3qxy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXY FirstGlance]. <br>		<table><tr><td colspan='2'>[[3qxy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SETD6 ([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">SETD6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3qxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qxy RCSB], [http://www.ebi.ac.uk/pdbsum/3qxy 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=3qxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qxy RCSB], [http://www.ebi.ac.uk/pdbsum/3qxy PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TF65_HUMAN TF65_HUMAN]] NF-kappa-B is a pleiotropic transcription factor present in almost all cell types and is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. NF-kappa-B is a homo- or heterodimeric complex formed by the Rel-like domain-containing proteins RELA/p65, RELB, NFKB1/p105, NFKB1/p50, REL and NFKB2/p52 and the heterodimeric p65-p50 complex appears to be most abundant one. The dimers bind at kappa-B sites in the DNA of their target genes and the individual dimers have distinct preferences for different kappa-B sites that they can bind with distinguishable affinity and specificity. Different dimer combinations act as transcriptional activators or repressors, respectively. NF-kappa-B is controlled by various mechanisms of post-translational modification and subcellular compartmentalization as well as by interactions with other cofactors or corepressors. NF-kappa-B complexes are held in the cytoplasm in an inactive state complexed with members of the NF-kappa-B inhibitor (I-kappa-B) family. In a conventional activation pathway, I-kappa-B is phosphorylated by I-kappa-B kinases (IKKs) in response to different activators, subsequently degraded thus liberating the active NF-kappa-B complex which translocates to the nucleus. NF-kappa-B heterodimeric p65-p50 and p65-c-Rel complexes are transcriptional activators. The NF-kappa-B p65-p65 complex appears to be involved in invasin-mediated activation of IL-8 expression. The inhibitory effect of I-kappa-B upon NF-kappa-B the cytoplasm is exerted primarily through the interaction with p65. p65 shows a weak DNA-binding site which could contribute directly to DNA binding in the NF-kappa-B complex. Associates with chromatin at the NF-kappa-B promoter region via association with DDX1.<ref>PMID:10928981</ref> <ref>PMID:12748188</ref> <ref>PMID:17000776</ref> <ref>PMID:17620405</ref> <ref>PMID:19058135</ref> <ref>PMID:20547752</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	Structural basis of SETD6-mediated regulation of the NF-kB network via methyl-lysine signaling.,Chang Y, Levy D, Horton JR, Peng J, Zhang X, Gozani O, Cheng X Nucleic Acids Res. 2011 Apr 22. PMID:21515635<ref>PMID:21515635</ref>		Structural basis of SETD6-mediated regulation of the NF-kB network via methyl-lysine signaling.,Chang Y, Levy D, Horton JR, Peng J, Zhang X, Gozani O, Cheng X Nucleic Acids Res. 2011 Apr 22. PMID:21515635<ref>PMID:21515635</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>

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	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Chang, Y.]]	+	[[Category: Chang, Y]]
-	[[Category: Cheng, X.]]	+	[[Category: Cheng, X]]
-	[[Category: Gozani, O.]]	+	[[Category: Gozani, O]]
-	[[Category: Horton, J R.]]	+	[[Category: Horton, J R]]
-	[[Category: Levy, D.]]	+	[[Category: Levy, D]]
-	[[Category: Peng, J.]]	+	[[Category: Peng, J]]
-	[[Category: Zhang, X.]]	+	[[Category: Zhang, X]]
	[[Category: Epigenetic]]		[[Category: Epigenetic]]
	[[Category: Nf-kb network via methyllysine signaling]]		[[Category: Nf-kb network via methyllysine signaling]]
	[[Category: Protein lysine methyltransferase]]		[[Category: Protein lysine methyltransferase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 04:51, 5 June 2014

OCA — Thu, 05 Jun 2014 04:51:56 GMT

←Older revision		Revision as of 04:51, 5 June 2014
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-	[[~~Image:~~3qxy.~~png~~\|~~left~~\|~~200px~~]]	+	==Human SETD6 in complex with RelA Lys310==
		+	<StructureSection load='3qxy' size='340' side='right' caption='[[3qxy]], [[Resolution\|resolution]] 2.09Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3qxy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXY FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SETD6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3qxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qxy RCSB], [http://www.ebi.ac.uk/pdbsum/3qxy PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	SET domain containing 6 (SETD6) monomethylates the RelA subunit of nuclear factor kappa B (NF-kappaB). The ankyrin repeats of G9a-like protein (GLP) recognizes RelA monomethylated at Lys310. Adjacent to Lys310 is Ser311, a known phosphorylation site of RelA. Ser311 phosphorylation inhibits Lys310 methylation by SETD6 as well as binding of Lys310me1 by GLP. The structure of SETD6 in complex with RelA peptide containing the methylation site, in the presence of S-adenosyl-l-methionine, reveals a V-like protein structure and suggests a model for NF-kappaB binding to SETD6. In addition, structural modeling of the GLP ankyrin repeats bound to Lys310me1 peptide provides insight into the molecular basis for inhibition of Lys310me1 binding by Ser311 phosphorylation. Together, these findings provide a structural explanation for a key cellular signaling pathway centered on RelA Lys310 methylation, which is generated by SETD6 and recognized by GLP, and incorporate a methylation-phosphorylation switch of adjacent lysine and serine residues. Finally, SETD6 is structurally similar to the Rubisco large subunit methyltransferase. Given the restriction of Rubisco to plant species, this particular appearance of the protein lysine methyltransferase has been evolutionarily well conserved.

-	<!--	+	Structural basis of SETD6-mediated regulation of the NF-kB network via methyl-lysine signaling.,Chang Y, Levy D, Horton JR, Peng J, Zhang X, Gozani O, Cheng X Nucleic Acids Res. 2011 Apr 22. PMID:21515635<ref>PMID:21515635</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3qxy"~~, ~~creates the "Structure Box" on the page.~~	+
-	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded)~~,	+
-	~~or leave the SCENE parameter empty for the default display~~.	+
-	-->	+
-	~~{{STRUCTURE_3qxy\| PDB=3qxy \| SCENE= }}~~	+

-	~~===Human SETD6 in complex with RelA Lys310===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-		+	==See Also==
-	~~<!--~~	+	*[[Histone methyltransferase\|Histone methyltransferase]]
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21515635}}, adds the Publication Abstract to the page~~	+	== References ==
-	~~(as it appears on PubMed at http://www.pubmed.gov), where 21515635 is the PubMed ID number.~~	+	<references/>
-	~~-->~~	+	__TOC__
-	~~{{ABSTRACT_PUBMED_21515635}}~~	+	</StructureSection>
-		+
-	==~~About this Structure~~==	+
-	[[~~3qxy~~]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXY OCA].	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021515635<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Chang, Y.]]		[[Category: Chang, Y.]]

OCA at 05:08, 10 August 2011

OCA — Wed, 10 Aug 2011 05:08:53 GMT

←Older revision		Revision as of 05:08, 10 August 2011
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-	[[Image:3qxy.~~jpg~~\|left\|200px]]	+	[[Image:3qxy.png\|left\|200px]]

	<!--		<!--
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	[[Category: Peng, J.]]		[[Category: Peng, J.]]
	[[Category: Zhang, X.]]		[[Category: Zhang, X.]]
		+	[[Category: Epigenetic]]
		+	[[Category: Nf-kb network via methyllysine signaling]]
		+	[[Category: Protein lysine methyltransferase]]
		+	[[Category: Transferase]]

OCA at 05:33, 25 May 2011

OCA — Wed, 25 May 2011 05:33:33 GMT

←Older revision		Revision as of 05:33, 25 May 2011
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-	~~'''Unreleased structure'''~~	+	[[Image:3qxy.jpg\|left\|200px]]

-	The ~~entry 3qxy~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3qxy", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3qxy\| PDB=3qxy \| SCENE= }}

-	~~Authors: Chang, Y., Levy, D., Horton, J.R., Peng, J., Zhang, X., Gozani, O., Cheng, X.~~	+	===Human SETD6 in complex with RelA Lys310===

-	~~Description~~: ~~Human SETD6 in complex~~ with ~~RelA Lys310~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21515635}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21515635 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21515635}}
		+
		+	==About this Structure==
		+	[[3qxy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXY OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021515635</ref><references group="xtra"/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Chang, Y.]]
		+	[[Category: Cheng, X.]]
		+	[[Category: Gozani, O.]]
		+	[[Category: Horton, J R.]]
		+	[[Category: Levy, D.]]
		+	[[Category: Peng, J.]]
		+	[[Category: Zhang, X.]]

OCA at 10:18, 21 April 2011

OCA — Thu, 21 Apr 2011 10:18:35 GMT

←Older revision		Revision as of 10:18, 21 April 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3qxy is ON HOLD	+	The entry 3qxy is ON HOLD until Paper Publication

	Authors: Chang, Y., Levy, D., Horton, J.R., Peng, J., Zhang, X., Gozani, O., Cheng, X.		Authors: Chang, Y., Levy, D., Horton, J.R., Peng, J., Zhang, X., Gozani, O., Cheng, X.

	Description: Human SETD6 in complex with RelA Lys310		Description: Human SETD6 in complex with RelA Lys310

OCA: Protected "3qxy" [edit=sysop:move=sysop]

OCA — Wed, 09 Mar 2011 06:10:40 GMT

Protected "3qxy" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:10, 9 March 2011

OCA: New page: '''Unreleased structure''' The entry 3qxy is ON HOLD Authors: Chang, Y., Levy, D., Horton, J.R., Peng, J., Zhang, X., Gozani, O., Cheng, X. Description: Human SETD6 in complex with Rel...

OCA — Wed, 09 Mar 2011 06:10:39 GMT

New page: '''Unreleased structure''' The entry 3qxy is ON HOLD Authors: Chang, Y., Levy, D., Horton, J.R., Peng, J., Zhang, X., Gozani, O., Cheng, X. Description: Human SETD6 in complex with Rel...

New page

'''Unreleased structure'''

The entry 3qxy is ON HOLD

Authors: Chang, Y., Levy, D., Horton, J.R., Peng, J., Zhang, X., Gozani, O., Cheng, X.

Description: Human SETD6 in complex with RelA Lys310