1gji - Revision history

OCA at 06:00, 3 April 2024

2024-04-03T06:00:14Z

←Older revision		Revision as of 06:00, 3 April 2024
Line 19:		Line 19:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gji ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gji ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	BACKGROUND: The proto-oncogene product c-Rel is a Rel/NF-kappaB family transcription factor that plays a critical role in lymphoid cell development and mediates CD28-induced expression of interleukin 2 (IL-2). The CD28 response element (CD28RE) in the IL-2 enhancer is nonameric and similar to the kappaB DNA target sites recognized by p65 homodimers. RESULTS: We have determined and refined the X-ray crystal structure of the c-Rel homodimer complexed to the CD28RE DNA site, 5'-AGAAATTCC-3', to 2.85 A resolution. The c-Rel homodimer binds CD28RE in a mode similar to that observed in the p65/IL-8 kappaB crystallographic complex. Binding studies reveal that the c-Rel homodimer recognizes the CD28RE with higher affinity as compared to other canonical kappaB sequences despite the nonconsensus A:T base pair at the 5' end of the CD28RE. Preferential recognition of the CD28RE by c-Rel results from the direct contacts between the protein and the DNA as well as intrasubunit interactions between the beta(f)-beta(g) loop in the dimerization domain and the DNA-contacting loop L1 of the N-terminal domain. Not only do these loops have different conformations in other Rel/DNA crystallographic complexes, but they also contain two of the five oncogenic point mutations found in v-Rel. CONCLUSIONS: The current structure indicates that a non-DNA-contacting loop in the dimerization domain and the DNA-contacting loop L1 may play critical roles in defining affinity and specificity. Two amino acid changes in these segments may account for the differential DNA binding by v-Rel as compared to that of c-Rel.
-
-	X-ray crystal structure of proto-oncogene product c-Rel bound to the CD28 response element of IL-2.,Huang DB, Chen YQ, Ruetsche M, Phelps CB, Ghosh G Structure. 2001 Aug;9(8):669-78. PMID:11587641<ref>PMID:11587641</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1gji" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 23:33, 27 December 2023

2023-12-27T23:33:13Z

←Older revision		Revision as of 23:33, 27 December 2023
Line 3:		Line 3:
	<StructureSection load='1gji' size='340' side='right'caption='[[1gji]], [[Resolution\|resolution]] 2.85Å' scene=''>		<StructureSection load='1gji' size='340' side='right'caption='[[1gji]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gji]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Chick Chick~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GJI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GJI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gji]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GJI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GJI 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=1gji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gji OCA], [https://pdbe.org/1gji PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gji RCSB], [https://www.ebi.ac.uk/pdbsum/1gji PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gji ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.85Å</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=1gji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gji OCA], [https://pdbe.org/1gji PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gji RCSB], [https://www.ebi.ac.uk/pdbsum/1gji PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gji ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/REL_CHICK REL_CHICK]] Proto-oncogene that may play a role in differentiation and lymphopoiesis. NF-kappa-B is a pleiotropic transcription factor which is present in almost all cell types and is involved in many biological processed 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. 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. The NF-kappa-B heterodimer RELA/p65-c-Rel is a transcriptional activator (By similarity).	+	[https://www.uniprot.org/uniprot/REL_CHICK REL_CHICK] Proto-oncogene that may play a role in differentiation and lymphopoiesis. NF-kappa-B is a pleiotropic transcription factor which is present in almost all cell types and is involved in many biological processed 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. 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. The NF-kappa-B heterodimer RELA/p65-c-Rel is a transcriptional activator (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Chick~~]]	+	[[Category: Gallus gallus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen~~, Y Q~~]]	+	[[Category: Chen YQ]]
-	[[Category: Ghosh, G]]	+	[[Category: Ghosh G]]
-	[[Category: Huang~~, D B~~]]	+	[[Category: Huang DB]]
-	[[Category: Phelps~~, C B~~]]	+	[[Category: Phelps CB]]
-	[[Category: Ruetsche, M]]	+	[[Category: Ruetsche M]]
-	~~[[Category: C-rel homodimer]]~~	+
-	~~[[Category: Nf-kb-dna complex]]~~	+
-	~~[[Category: Transcription factor]]~~	+
-	~~[[Category: Transcription-dna complex~~]]	+

OCA at 11:24, 28 July 2021

2021-07-28T11:24:43Z

←Older revision		Revision as of 11:24, 28 July 2021
Line 3:		Line 3:
	<StructureSection load='1gji' size='340' side='right'caption='[[1gji]], [[Resolution\|resolution]] 2.85Å' scene=''>		<StructureSection load='1gji' size='340' side='right'caption='[[1gji]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gji]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GJI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1GJI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gji]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GJI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GJI 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=1gji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gji OCA], [~~http~~://pdbe.org/1gji PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1gji RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1gji PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1gji 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=1gji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gji OCA], [https://pdbe.org/1gji PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gji RCSB], [https://www.ebi.ac.uk/pdbsum/1gji PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gji ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/REL_CHICK REL_CHICK]] Proto-oncogene that may play a role in differentiation and lymphopoiesis. NF-kappa-B is a pleiotropic transcription factor which is present in almost all cell types and is involved in many biological processed 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. 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. The NF-kappa-B heterodimer RELA/p65-c-Rel is a transcriptional activator (By similarity).	+	[[https://www.uniprot.org/uniprot/REL_CHICK REL_CHICK]] Proto-oncogene that may play a role in differentiation and lymphopoiesis. NF-kappa-B is a pleiotropic transcription factor which is present in almost all cell types and is involved in many biological processed 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. 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. The NF-kappa-B heterodimer RELA/p65-c-Rel is a transcriptional activator (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:32, 23 October 2019

2019-10-23T08:32:53Z

←Older revision		Revision as of 08:32, 23 October 2019
Line 1:		Line 1:

	==Crystal structure of c-Rel bound to DNA==		==Crystal structure of c-Rel bound to DNA==
-	<StructureSection load='1gji' size='340' side='right' caption='[[1gji]], [[Resolution\|resolution]] 2.85Å' scene=''>	+	<StructureSection load='1gji' size='340' side='right'caption='[[1gji]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1gji]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GJI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GJI FirstGlance]. <br>		<table><tr><td colspan='2'>[[1gji]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GJI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GJI FirstGlance]. <br>
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Chick]]		[[Category: Chick]]
		+	[[Category: Large Structures]]
	[[Category: Chen, Y Q]]		[[Category: Chen, Y Q]]
	[[Category: Ghosh, G]]		[[Category: Ghosh, G]]

OCA at 06:20, 3 January 2018

2018-01-03T06:20:12Z

←Older revision		Revision as of 06:20, 3 January 2018
Line 1:		Line 1:
		+
	==Crystal structure of c-Rel bound to DNA==		==Crystal structure of c-Rel bound to DNA==
	<StructureSection load='1gji' size='340' side='right' caption='[[1gji]], [[Resolution\|resolution]] 2.85Å' scene=''>		<StructureSection load='1gji' size='340' side='right' caption='[[1gji]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1gji]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GJI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GJI FirstGlance]. <br>		<table><tr><td colspan='2'>[[1gji]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GJI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GJI 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=1gji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gji OCA], [http://pdbe.org/1gji PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gji RCSB], [http://www.ebi.ac.uk/pdbsum/1gji PDBsum]</span></td></tr>	+	</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=1gji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gji OCA], [http://pdbe.org/1gji PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gji RCSB], [http://www.ebi.ac.uk/pdbsum/1gji PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1gji ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gj/1gji_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gj/1gji_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 23:00, 8 February 2016

2016-02-08T23:00:09Z

←Older revision		Revision as of 23:00, 8 February 2016
Line 15:		Line 15:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gji ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:11, 10 September 2015

2015-09-10T16:11:25Z

←Older revision		Revision as of 16:11, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1gji' size='340' side='right' caption='[[1gji]], [[Resolution\|resolution]] 2.85Å' scene=''>		<StructureSection load='1gji' size='340' side='right' caption='[[1gji]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gji]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Gallus_gallus Gallus gallus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GJI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GJI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gji]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GJI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GJI 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=1gji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gji OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gji RCSB], [http://www.ebi.ac.uk/pdbsum/1gji PDBsum]</span></td></tr>	+	</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=1gji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gji OCA], [http://pdbe.org/1gji PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gji RCSB], [http://www.ebi.ac.uk/pdbsum/1gji PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 25:
	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 1gji" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Gallus gallus~~]]	+	[[Category: Chick]]
	[[Category: Chen, Y Q]]		[[Category: Chen, Y Q]]
	[[Category: Ghosh, G]]		[[Category: Ghosh, G]]

OCA at 02:43, 25 December 2014

2014-12-25T02:43:43Z

←Older revision		Revision as of 02:43, 25 December 2014
Line 5:		Line 5:
	</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=1gji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gji OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gji RCSB], [http://www.ebi.ac.uk/pdbsum/1gji PDBsum]</span></td></tr>		</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=1gji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gji OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gji RCSB], [http://www.ebi.ac.uk/pdbsum/1gji PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/REL_CHICK REL_CHICK]] Proto-oncogene that may play a role in differentiation and lymphopoiesis. NF-kappa-B is a pleiotropic transcription factor which is present in almost all cell types and is involved in many biological processed 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. 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. The NF-kappa-B heterodimer RELA/p65-c-Rel is a transcriptional activator (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 18:21, 22 December 2014

2014-12-22T18:21:18Z

←Older revision		Revision as of 18:21, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1gji]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GJI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GJI FirstGlance]. <br>		<table><tr><td colspan='2'>[[1gji]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GJI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GJI FirstGlance]. <br>
-	</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=1gji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gji OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gji RCSB], [http://www.ebi.ac.uk/pdbsum/1gji PDBsum]</span></td></tr>	+	</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=1gji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gji OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gji RCSB], [http://www.ebi.ac.uk/pdbsum/1gji PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
-	[[Category: Chen, Y Q.]]	+	[[Category: Chen, Y Q]]
-	[[Category: Ghosh, G.]]	+	[[Category: Ghosh, G]]
-	[[Category: Huang, D B.]]	+	[[Category: Huang, D B]]
-	[[Category: Phelps, C B.]]	+	[[Category: Phelps, C B]]
-	[[Category: Ruetsche, M.]]	+	[[Category: Ruetsche, M]]
	[[Category: C-rel homodimer]]		[[Category: C-rel homodimer]]
	[[Category: Nf-kb-dna complex]]		[[Category: Nf-kb-dna complex]]
	[[Category: Transcription factor]]		[[Category: Transcription factor]]
	[[Category: Transcription-dna complex]]		[[Category: Transcription-dna complex]]

OCA at 08:24, 28 September 2014

2014-09-28T08:24:52Z

←Older revision		Revision as of 08:24, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1gji.~~png\|left~~\|200px]]	+	==Crystal structure of c-Rel bound to DNA==
		+	<StructureSection load='1gji' size='340' side='right' caption='[[1gji]], [[Resolution\|resolution]] 2.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1gji]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GJI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GJI FirstGlance]. <br>
		+	</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=1gji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gji OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gji RCSB], [http://www.ebi.ac.uk/pdbsum/1gji PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gj/1gji_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: The proto-oncogene product c-Rel is a Rel/NF-kappaB family transcription factor that plays a critical role in lymphoid cell development and mediates CD28-induced expression of interleukin 2 (IL-2). The CD28 response element (CD28RE) in the IL-2 enhancer is nonameric and similar to the kappaB DNA target sites recognized by p65 homodimers. RESULTS: We have determined and refined the X-ray crystal structure of the c-Rel homodimer complexed to the CD28RE DNA site, 5'-AGAAATTCC-3', to 2.85 A resolution. The c-Rel homodimer binds CD28RE in a mode similar to that observed in the p65/IL-8 kappaB crystallographic complex. Binding studies reveal that the c-Rel homodimer recognizes the CD28RE with higher affinity as compared to other canonical kappaB sequences despite the nonconsensus A:T base pair at the 5' end of the CD28RE. Preferential recognition of the CD28RE by c-Rel results from the direct contacts between the protein and the DNA as well as intrasubunit interactions between the beta(f)-beta(g) loop in the dimerization domain and the DNA-contacting loop L1 of the N-terminal domain. Not only do these loops have different conformations in other Rel/DNA crystallographic complexes, but they also contain two of the five oncogenic point mutations found in v-Rel. CONCLUSIONS: The current structure indicates that a non-DNA-contacting loop in the dimerization domain and the DNA-contacting loop L1 may play critical roles in defining affinity and specificity. Two amino acid changes in these segments may account for the differential DNA binding by v-Rel as compared to that of c-Rel.

-	~~{{STRUCTURE_1gji\| PDB=1gji \| SCENE= }}~~	+	X-ray crystal structure of proto-oncogene product c-Rel bound to the CD28 response element of IL-2.,Huang DB, Chen YQ, Ruetsche M, Phelps CB, Ghosh G Structure. 2001 Aug;9(8):669-78. PMID:11587641<ref>PMID:11587641</ref>

-	~~===Crystal structure~~ of ~~c-Rel bound to DNA===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11587641}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1gji]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Gallus_gallus Gallus gallus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1GJI OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:011587641<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
	[[Category: Chen, Y Q.]]		[[Category: Chen, Y Q.]]