2h1e - Revision history

OCA at 09:50, 30 August 2023

OCA — Wed, 30 Aug 2023 09:50:28 GMT

←Older revision		Revision as of 09:50, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2h1e' size='340' side='right'caption='[[2h1e]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2h1e' size='340' side='right'caption='[[2h1e]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2h1e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H1E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H1E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2h1e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H1E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H1E FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]], [[2b2y\|2b2y]], [[1kne\|1kne]], [[1pdq\|1pdq]], [[1guw\|1guw]]</div></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]] 2.2Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">CHD1 ([https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=4932 ATCC 18824])~~</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=2h1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h1e OCA], [https://pdbe.org/2h1e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h1e RCSB], [https://www.ebi.ac.uk/pdbsum/2h1e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h1e 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=2h1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h1e OCA], [https://pdbe.org/2h1e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h1e RCSB], [https://www.ebi.ac.uk/pdbsum/2h1e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h1e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CHD1_YEAST CHD1_YEAST]] ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK. It recognizes H3K4me. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. Acts in opposition to the FACT complex in regulating polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the pol I transcription termination step. Regulates negatively DNA replication. Not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome.<ref>PMID:10026213</ref> <ref>PMID:10811623</ref> <ref>PMID:12682017</ref> <ref>PMID:14585955</ref> <ref>PMID:15647753</ref> <ref>PMID:16606615</ref> <ref>PMID:16468993</ref> <ref>PMID:17949749</ref> <ref>PMID:17620414</ref> <ref>PMID:17259992</ref> <ref>PMID:18245327</ref>	+	[https://www.uniprot.org/uniprot/CHD1_YEAST CHD1_YEAST] ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK. It recognizes H3K4me. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. Acts in opposition to the FACT complex in regulating polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the pol I transcription termination step. Regulates negatively DNA replication. Not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome.<ref>PMID:10026213</ref> <ref>PMID:10811623</ref> <ref>PMID:12682017</ref> <ref>PMID:14585955</ref> <ref>PMID:15647753</ref> <ref>PMID:16606615</ref> <ref>PMID:16468993</ref> <ref>PMID:17949749</ref> <ref>PMID:17620414</ref> <ref>PMID:17259992</ref> <ref>PMID:18245327</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~IV, J F.Flanagan~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: ~~Khorasanizadeh, S~~]]	+	[[Category: Flanagan IV JF]]
-	[[Category: ~~Chd1]]~~	+	[[Category: Khorasanizadeh S]]
-	~~[[Category: Chromodomain]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Tandem chromodomain]]~~	+
-	~~[[Category: Three-stranded antiparallel b-sheet~~]]	+

OCA at 07:28, 17 March 2021

OCA — Wed, 17 Mar 2021 07:28:52 GMT

←Older revision		Revision as of 07:28, 17 March 2021
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	==Tandem chromodomains of budding yeast CHD1==		==Tandem chromodomains of budding yeast CHD1==
-	<StructureSection load='2h1e' size='340' side='right' caption='[[2h1e]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='2h1e' size='340' side='right'caption='[[2h1e]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2h1e]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H1E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2H1E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2h1e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H1E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H1E FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]], [[2b2y\|2b2y]], [[1kne\|1kne]], [[1pdq\|1pdq]], [[1guw\|1guw]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]], [[2b2y\|2b2y]], [[1kne\|1kne]], [[1pdq\|1pdq]], [[1guw\|1guw]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CHD1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CHD1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=2h1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h1e OCA], [~~http~~://pdbe.org/2h1e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2h1e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2h1e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2h1e 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=2h1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h1e OCA], [https://pdbe.org/2h1e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h1e RCSB], [https://www.ebi.ac.uk/pdbsum/2h1e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h1e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CHD1_YEAST CHD1_YEAST]] ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK. It recognizes H3K4me. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. Acts in opposition to the FACT complex in regulating polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the pol I transcription termination step. Regulates negatively DNA replication. Not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome.<ref>PMID:10026213</ref> <ref>PMID:10811623</ref> <ref>PMID:12682017</ref> <ref>PMID:14585955</ref> <ref>PMID:15647753</ref> <ref>PMID:16606615</ref> <ref>PMID:16468993</ref> <ref>PMID:17949749</ref> <ref>PMID:17620414</ref> <ref>PMID:17259992</ref> <ref>PMID:18245327</ref>	+	[[https://www.uniprot.org/uniprot/CHD1_YEAST CHD1_YEAST]] ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK. It recognizes H3K4me. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. Acts in opposition to the FACT complex in regulating polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the pol I transcription termination step. Regulates negatively DNA replication. Not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome.<ref>PMID:10026213</ref> <ref>PMID:10811623</ref> <ref>PMID:12682017</ref> <ref>PMID:14585955</ref> <ref>PMID:15647753</ref> <ref>PMID:16606615</ref> <ref>PMID:16468993</ref> <ref>PMID:17949749</ref> <ref>PMID:17620414</ref> <ref>PMID:17259992</ref> <ref>PMID:18245327</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h1/2h1e_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h1/2h1e_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>
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	</div>		</div>
	<div class="pdbe-citations 2h1e" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2h1e" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Helicase 3D structures\|Helicase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
		+	[[Category: Large Structures]]
	[[Category: IV, J F.Flanagan]]		[[Category: IV, J F.Flanagan]]
	[[Category: Khorasanizadeh, S]]		[[Category: Khorasanizadeh, S]]

OCA at 08:04, 18 October 2017

OCA — Wed, 18 Oct 2017 08:04:43 GMT

←Older revision		Revision as of 08:04, 18 October 2017
Line 1:		Line 1:
		+
	==Tandem chromodomains of budding yeast CHD1==		==Tandem chromodomains of budding yeast CHD1==
	<StructureSection load='2h1e' size='340' side='right' caption='[[2h1e]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2h1e' size='340' side='right' caption='[[2h1e]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]], [[2b2y\|2b2y]], [[1kne\|1kne]], [[1pdq\|1pdq]], [[1guw\|1guw]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]], [[2b2y\|2b2y]], [[1kne\|1kne]], [[1pdq\|1pdq]], [[1guw\|1guw]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CHD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CHD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=2h1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h1e OCA], [http://pdbe.org/2h1e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2h1e RCSB], [http://www.ebi.ac.uk/pdbsum/2h1e 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=2h1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h1e OCA], [http://pdbe.org/2h1e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2h1e RCSB], [http://www.ebi.ac.uk/pdbsum/2h1e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2h1e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2h1e" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2h1e" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Helicase\|Helicase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:28, 10 February 2016

OCA — Wed, 10 Feb 2016 08:28:16 GMT

←Older revision		Revision as of 08:28, 10 February 2016
Line 17:		Line 17:
	<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=2h1e ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:05, 11 September 2015

OCA — Fri, 11 Sep 2015 07:05:43 GMT

←Older revision		Revision as of 07:05, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2h1e' size='340' side='right' caption='[[2h1e]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2h1e' size='340' side='right' caption='[[2h1e]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2h1e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H1E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H1E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2h1e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H1E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H1E FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]], [[2b2y\|2b2y]], [[1kne\|1kne]], [[1pdq\|1pdq]], [[1guw\|1guw]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]], [[2b2y\|2b2y]], [[1kne\|1kne]], [[1pdq\|1pdq]], [[1guw\|1guw]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CHD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ~~Saccharomyces cerevisiae~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CHD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=2h1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h1e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2h1e RCSB], [http://www.ebi.ac.uk/pdbsum/2h1e 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=2h1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h1e OCA], [http://pdbe.org/2h1e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2h1e RCSB], [http://www.ebi.ac.uk/pdbsum/2h1e PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 2h1e" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saccharomyces cerevisiae~~]]	+	[[Category: Atcc 18824]]
	[[Category: IV, J F.Flanagan]]		[[Category: IV, J F.Flanagan]]
	[[Category: Khorasanizadeh, S]]		[[Category: Khorasanizadeh, S]]

OCA at 12:59, 25 December 2014

OCA — Thu, 25 Dec 2014 12:59:57 GMT

←Older revision		Revision as of 12:59, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2h1e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H1E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H1E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2h1e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H1E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H1E FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]], [[2b2y\|2b2y]], [[1kne\|1kne]], [[1pdq\|1pdq]], [[1guw\|1guw]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]], [[2b2y\|2b2y]], [[1kne\|1kne]], [[1pdq\|1pdq]], [[1guw\|1guw]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CHD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CHD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=2h1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h1e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2h1e RCSB], [http://www.ebi.ac.uk/pdbsum/2h1e 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=2h1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h1e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2h1e RCSB], [http://www.ebi.ac.uk/pdbsum/2h1e PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CHD1_YEAST CHD1_YEAST]] ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK. It recognizes H3K4me. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. Acts in opposition to the FACT complex in regulating polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the pol I transcription termination step. Regulates negatively DNA replication. Not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome.<ref>PMID:10026213</ref> <ref>PMID:10811623</ref> <ref>PMID:12682017</ref> <ref>PMID:14585955</ref> <ref>PMID:15647753</ref> <ref>PMID:16606615</ref> <ref>PMID:16468993</ref> <ref>PMID:17949749</ref> <ref>PMID:17620414</ref> <ref>PMID:17259992</ref> <ref>PMID:18245327</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: IV, J F.Flanagan.]]	+	[[Category: IV, J F.Flanagan]]
-	[[Category: Khorasanizadeh, S.]]	+	[[Category: Khorasanizadeh, S]]
	[[Category: Chd1]]		[[Category: Chd1]]
	[[Category: Chromodomain]]		[[Category: Chromodomain]]

OCA at 04:08, 29 September 2014

OCA — Mon, 29 Sep 2014 04:08:49 GMT

←Older revision		Revision as of 04:08, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2h1e.~~png~~\|~~left~~\|200px]]	+	==Tandem chromodomains of budding yeast CHD1==
		+	<StructureSection load='2h1e' size='340' side='right' caption='[[2h1e]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2h1e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H1E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H1E FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]], [[2b2y\|2b2y]], [[1kne\|1kne]], [[1pdq\|1pdq]], [[1guw\|1guw]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CHD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=2h1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h1e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2h1e RCSB], [http://www.ebi.ac.uk/pdbsum/2h1e 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/h1/2h1e_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 ==
		+	Double chromodomains occur in CHD proteins, which are ATP-dependent chromatin remodeling factors implicated in RNA polymerase II transcription regulation. Biochemical studies suggest important differences in the histone H3 tail binding of different CHD chromodomains. In human and Drosophila, CHD1 double chromodomains bind lysine 4-methylated histone H3 tail, which is a hallmark of transcriptionally active chromatin in all eukaryotes. Here, we present the crystal structure of the yeast CHD1 double chromodomains, and pinpoint their differences with that of the human CHD1 double chromodomains. The most conserved residues in these double chromodomains are the two chromoboxes that orient adjacently. Only a subset of CHD chromoboxes can form an aromatic cage for methyllysine binding, and methyllysine binding requires correctly oriented inserts. These factors preclude yeast CHD1 double chromodomains from interacting with the histone H3 tail. Despite great sequence similarity between the human CHD1 and CHD2 chromodomains, variation within an insert likely prevents CHD2 double chromodomains from binding lysine 4-methylated histone H3 tail as efficiently as in CHD1. By using the available structural and biochemical data we highlight the evolutionary specialization of CHD double chromodomains, and provide insights about their targeting capacities.

-	~~{{STRUCTURE_2h1e\| PDB=2h1e \| SCENE= }}~~	+	Molecular implications of evolutionary differences in CHD double chromodomains.,Flanagan JF, Blus BJ, Kim D, Clines KL, Rastinejad F, Khorasanizadeh S J Mol Biol. 2007 Jun 1;369(2):334-42. Epub 2007 Mar 19. PMID:17433364<ref>PMID:17433364</ref>

-	~~===Tandem chromodomains~~ of ~~budding yeast CHD1===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17433364}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2h1e]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2H1E OCA].~~	+

	==See Also==		==See Also==
	*[[Helicase\|Helicase]]		*[[Helicase\|Helicase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017433364<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: IV, J F.Flanagan.]]		[[Category: IV, J F.Flanagan.]]

OCA at 16:58, 20 October 2012

OCA — Sat, 20 Oct 2012 16:58:20 GMT

←Older revision		Revision as of 16:58, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2h1e]] is a 2 chain structure ~~of [[Helicase]]~~ with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H1E OCA].	+	[[2h1e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H1E OCA].

	==See Also==		==See Also==

OCA: Protected "2h1e" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 23:25:05 GMT

Protected "2h1e" [edit=sysop:move=sysop]

←Older revision

Revision as of 23:25, 26 July 2012

OCA at 23:25, 26 July 2012

OCA — Thu, 26 Jul 2012 23:25:03 GMT

←Older revision		Revision as of 23:25, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2h1e.png\|left\|200px]]		[[Image:2h1e.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2h1e", 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_2h1e\| PDB=2h1e \| SCENE= }}		{{STRUCTURE_2h1e\| PDB=2h1e \| SCENE= }}

	===Tandem chromodomains of budding yeast CHD1===		===Tandem chromodomains of budding yeast CHD1===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17433364}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17433364 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17433364}}		{{ABSTRACT_PUBMED_17433364}}

	==About this Structure==		==About this Structure==
-	~~2H1E~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H1E OCA].	+	[[2h1e]] is a 2 chain structure of [[Helicase]] with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H1E OCA].
		+
		+	==See Also==
		+	*[[Helicase\|Helicase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17433364~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017433364</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: IV, J F.Flanagan.]]		[[Category: IV, J F.Flanagan.]]
Line 29:		Line 20:
	[[Category: Chd1]]		[[Category: Chd1]]
	[[Category: Chromodomain]]		[[Category: Chromodomain]]
		+	[[Category: Hydrolase]]
	[[Category: Tandem chromodomain]]		[[Category: Tandem chromodomain]]
	[[Category: Three-stranded antiparallel b-sheet]]		[[Category: Three-stranded antiparallel b-sheet]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 16:50:03 2009''