5u4k - Revision history

OCA at 10:05, 22 May 2024

OCA — Wed, 22 May 2024 10:05:28 GMT

←Older revision		Revision as of 10:05, 22 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5u4k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U4K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U4K FirstGlance]. <br>		<table><tr><td colspan='2'>[[5u4k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U4K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U4K 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=5u4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u4k OCA], [https://pdbe.org/5u4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u4k RCSB], [https://www.ebi.ac.uk/pdbsum/5u4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u4k 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=5u4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u4k OCA], [https://pdbe.org/5u4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u4k RCSB], [https://www.ebi.ac.uk/pdbsum/5u4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u4k ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 12:01, 1 February 2023

OCA — Wed, 01 Feb 2023 12:01:50 GMT

←Older revision		Revision as of 12:01, 1 February 2023
Line 1:		Line 1:

	==NMR structure of the complex between the KIX domain of CBP and the transactivation domain 1 of p65==		==NMR structure of the complex between the KIX domain of CBP and the transactivation domain 1 of p65==
-	<StructureSection load='5u4k' size='340' side='right'caption='[[5u4k~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='5u4k' size='340' side='right'caption='[[5u4k]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u4k]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U4K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5U4K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u4k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U4K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U4K FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5u4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u4k OCA], [~~http~~://pdbe.org/5u4k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5u4k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5u4k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5u4k ProSAT]</span></td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5u4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u4k OCA], [https://pdbe.org/5u4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u4k RCSB], [https://www.ebi.ac.uk/pdbsum/5u4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u4k 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>	+	[https://www.uniprot.org/uniprot/CBP_MOUSE CBP_MOUSE] Acetylates histones, giving a specific tag for transcriptional activation. Also acetylates non-histone proteins, like NCOA3 and FOXO1. Binds specifically to phosphorylated CREB and enhances its transcriptional activity toward cAMP-responsive genes. Acts as a coactivator of ALX1 in the presence of EP300 (By similarity).<ref>PMID:10207073</ref> <ref>PMID:11701890</ref> <ref>PMID:15220471</ref> <ref>PMID:16287980</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arseneault, G]]	+	[[Category: Mus musculus]]
-	[[Category: Chabot~~, P R~~]]	+	[[Category: Arseneault G]]
-	[[Category: Cyr, N]]	+	[[Category: Chabot PR]]
-	[[Category: Lecoq, L]]	+	[[Category: Cyr N]]
-	[[Category: Omichinski~~, J G~~]]	+	[[Category: Lecoq L]]
-	[[Category: Raiola, L]]	+	[[Category: Omichinski JG]]
-	~~[[Category: Nf-kb]]~~	+	[[Category: Raiola L]]
-	~~[[Category: P300-cbp coactivator family]]~~	+
-	~~[[Category: Transactivation domain]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 12:26, 23 September 2020

OCA — Wed, 23 Sep 2020 12:26:32 GMT

←Older revision		Revision as of 12:26, 23 September 2020
Line 1:		Line 1:

	==NMR structure of the complex between the KIX domain of CBP and the transactivation domain 1 of p65==		==NMR structure of the complex between the KIX domain of CBP and the transactivation domain 1 of p65==
-	<StructureSection load='5u4k' size='340' side='right' caption='[[5u4k]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='5u4k' size='340' side='right'caption='[[5u4k]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u4k]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U4K OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5U4K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u4k]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U4K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5U4K FirstGlance]. <br>
-	</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=5u4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u4k OCA], [http://pdbe.org/5u4k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u4k RCSB], [http://www.ebi.ac.uk/pdbsum/5u4k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u4k ProSAT]</span></td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5u4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u4k OCA], [http://pdbe.org/5u4k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u4k RCSB], [http://www.ebi.ac.uk/pdbsum/5u4k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u4k ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5u4k" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5u4k" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[CREB-binding protein 3D structures\|CREB-binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Arseneault, G]]		[[Category: Arseneault, G]]
	[[Category: Chabot, P R]]		[[Category: Chabot, P R]]

OCA at 06:52, 5 April 2017

OCA — Wed, 05 Apr 2017 06:52:05 GMT

←Older revision		Revision as of 06:52, 5 April 2017
Line 8:		Line 8:
	== 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/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;">
		+	== Publication Abstract from PubMed ==
		+	p65 is a member of the NF-kappaB family of transcriptional regulatory proteins that functions as the activating component of the p65-p50 heterodimer. Through its acidic transactivation domain (TAD), p65 has the capacity to form interactions with several different transcriptional regulatory proteins, including TFIIB, TFIIH, CREB-binding protein (CBP)/p300 and TAFII31. Like other acidic TADs, the p65 TAD contains two subdomains (p65TA1 and p65TA2) that interact with different regulatory factors depending on the target gene. Despite its role in controlling numerous NF-kappaB target genes, there are no high-resolution structures of p65TA1 bound to a target transcriptional regulatory factor. In this work, we characterize the interaction of p65TA1 with two factors, the Tfb1/p62 subunit of TFIIH and the KIX domain of CBP. In these complexes, p65TA1 transitions into a helical conformation that includes its characteristic PhiXXPhiPhi motif (Phi = hydrophobic amino acid). Structural and functional studies demonstrate that the two binding interfaces are primarily stabilized by three hydrophobic amino acids within the PhiXXPhiPhi motif and these residues are also crucial to its ability to activate transcription. Taken together, the results provide an atomic level description of how p65TA1 is able to bind different transcriptional regulatory factors needed to activate NF-kappaB target genes.
		+
		+	Structural characterization of interactions between transactivation domain 1 of the p65 subunit of NF-kappaB and transcription regulatory factors.,Lecoq L, Raiola L, Chabot PR, Cyr N, Arseneault G, Legault P, Omichinski JG Nucleic Acids Res. 2017 Feb 28. doi: 10.1093/nar/gkx146. PMID:28334776<ref>PMID:28334776</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5u4k" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 19:19, 11 March 2017

OCA — Sat, 11 Mar 2017 19:19:17 GMT

←Older revision		Revision as of 19:19, 11 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5u4k is ~~ON HOLD~~	+	==NMR structure of the complex between the KIX domain of CBP and the transactivation domain 1 of p65==
-		+	<StructureSection load='5u4k' size='340' side='right' caption='[[5u4k]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5u4k]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U4K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U4K FirstGlance]. <br>
-	~~Description~~:	+	</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=5u4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u4k OCA], [http://pdbe.org/5u4k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u4k RCSB], [http://www.ebi.ac.uk/pdbsum/5u4k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u4k ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</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>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arseneault, G]]
		+	[[Category: Chabot, P R]]
		+	[[Category: Cyr, N]]
		+	[[Category: Lecoq, L]]
		+	[[Category: Omichinski, J G]]
		+	[[Category: Raiola, L]]
		+	[[Category: Nf-kb]]
		+	[[Category: P300-cbp coactivator family]]
		+	[[Category: Transactivation domain]]
		+	[[Category: Transcription]]

OCA: Protected "5u4k" [edit=sysop:move=sysop]

OCA — Thu, 15 Dec 2016 17:39:58 GMT

Protected "5u4k" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:39, 15 December 2016

OCA: New page: '''Unreleased structure''' The entry 5u4k is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 15 Dec 2016 17:39:57 GMT

New page: '''Unreleased structure''' The entry 5u4k is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5u4k is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]