2b2y - Revision history

OCA at 07:33, 23 August 2023

OCA — Wed, 23 Aug 2023 07:33:08 GMT

←Older revision		Revision as of 07:33, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='2b2y' size='340' side='right'caption='[[2b2y]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='2b2y' size='340' side='right'caption='[[2b2y]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2b2y]] is a 3 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=2B2Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B2Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2b2y]] is a 3 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=2B2Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B2Y 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;'>[[1kna\|1kna]], [[1kne\|1kne]], [[1q3l\|1q3l]], [[1pdq\|1pdq]], [[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]]</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]] 2.35Å</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=9606 HUMAN])~~</td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2b2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b2y OCA], [https://pdbe.org/2b2y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b2y RCSB], [https://www.ebi.ac.uk/pdbsum/2b2y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b2y 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=2b2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b2y OCA], [https://pdbe.org/2b2y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b2y RCSB], [https://www.ebi.ac.uk/pdbsum/2b2y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b2y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CHD1_HUMAN CHD1_HUMAN]] ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase 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. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Functions to modulate the efficiency of pre-mRNA splicing in part through physical bridging of spliceosomal components to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells.<ref>PMID:18042460</ref>	+	[https://www.uniprot.org/uniprot/CHD1_HUMAN CHD1_HUMAN] ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase 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. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Functions to modulate the efficiency of pre-mRNA splicing in part through physical bridging of spliceosomal components to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells.<ref>PMID:18042460</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: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chruszcz, M]]	+	[[Category: Chruszcz M]]
-	[[Category: Clines~~, K L~~]]	+	[[Category: Clines KL]]
-	[[Category: Cymborowski, M]]	+	[[Category: Cymborowski M]]
-	[[Category: IV~~, J F.Flanagan~~]]	+	[[Category: Flanagan IV JF]]
-	[[Category: Khorasanizadeh, S]]	+	[[Category: Khorasanizadeh S]]
-	[[Category: Kim, Y]]	+	[[Category: Kim Y]]
-	[[Category: Mi, L Z]]	+	[[Category: Mi L-Z]]
-	[[Category: Minor, W]]	+	[[Category: Minor W]]
-	[[Category: Rastinejad, F]]	+	[[Category: Rastinejad F]]
-	~~[[Category: Alpha helix linker]]~~	+
-	~~[[Category: Chd]]~~	+
-	~~[[Category: Chromodomain]]~~	+
-	~~[[Category: Peptide binding protein]]~~	+
-	~~[[Category: Three stranded antiparallel beta sheet~~]]	+

OCA at 11:33, 3 February 2021

OCA — Wed, 03 Feb 2021 11:33:09 GMT

←Older revision		Revision as of 11:33, 3 February 2021
Line 1:		Line 1:

	==Tandem chromodomains of human CHD1==		==Tandem chromodomains of human CHD1==
-	<StructureSection load='2b2y' size='340' side='right' caption='[[2b2y]], [[Resolution\|resolution]] 2.35Å' scene=''>	+	<StructureSection load='2b2y' size='340' side='right'caption='[[2b2y]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2b2y]] is a 3 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=2B2Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2B2Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2b2y]] is a 3 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=2B2Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B2Y FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kna\|1kna]], [[1kne\|1kne]], [[1q3l\|1q3l]], [[1pdq\|1pdq]], [[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]]</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;'>[[1kna\|1kna]], [[1kne\|1kne]], [[1q3l\|1q3l]], [[1pdq\|1pdq]], [[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]]</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=9606 HUMAN])</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=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=2b2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b2y OCA], [~~http~~://pdbe.org/2b2y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2b2y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2b2y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2b2y 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=2b2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b2y OCA], [https://pdbe.org/2b2y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b2y RCSB], [https://www.ebi.ac.uk/pdbsum/2b2y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b2y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CHD1_HUMAN CHD1_HUMAN]] ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase 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. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Functions to modulate the efficiency of pre-mRNA splicing in part through physical bridging of spliceosomal components to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells.<ref>PMID:18042460</ref>	+	[[https://www.uniprot.org/uniprot/CHD1_HUMAN CHD1_HUMAN]] ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase 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. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Functions to modulate the efficiency of pre-mRNA splicing in part through physical bridging of spliceosomal components to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells.<ref>PMID:18042460</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/b2/2b2y_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b2/2b2y_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>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2b2y" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2b2y" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Chromodomain-helicase-DNA-binding protein 3D structures\|Chromodomain-helicase-DNA-binding protein 3D structures]]
		+	*[[Helicase 3D structures\|Helicase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Chruszcz, M]]		[[Category: Chruszcz, M]]
	[[Category: Clines, K L]]		[[Category: Clines, K L]]

OCA at 14:47, 12 October 2017

OCA — Thu, 12 Oct 2017 14:47:23 GMT

←Older revision		Revision as of 14:47, 12 October 2017
Line 1:		Line 1:
		+
	==Tandem chromodomains of human CHD1==		==Tandem chromodomains of human CHD1==
	<StructureSection load='2b2y' size='340' side='right' caption='[[2b2y]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='2b2y' size='340' side='right' caption='[[2b2y]], [[Resolution\|resolution]] 2.35Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kna\|1kna]], [[1kne\|1kne]], [[1q3l\|1q3l]], [[1pdq\|1pdq]], [[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kna\|1kna]], [[1kne\|1kne]], [[1q3l\|1q3l]], [[1pdq\|1pdq]], [[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]]</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=9606 HUMAN])</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=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=2b2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b2y OCA], [http://pdbe.org/2b2y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2b2y RCSB], [http://www.ebi.ac.uk/pdbsum/2b2y 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=2b2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b2y OCA], [http://pdbe.org/2b2y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2b2y RCSB], [http://www.ebi.ac.uk/pdbsum/2b2y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2b2y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	<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=2b2y ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2b2y" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2b2y" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Chromodomain-helicase-DNA-binding protein\|Chromodomain-helicase-DNA-binding protein]]
-	*[[Helicase\|Helicase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:38, 11 September 2015

OCA — Fri, 11 Sep 2015 09:38:42 GMT

←Older revision		Revision as of 09:38, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2b2y' size='340' side='right' caption='[[2b2y]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='2b2y' size='340' side='right' caption='[[2b2y]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2b2y]] is a 3 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=2B2Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2B2Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2b2y]] is a 3 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=2B2Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2B2Y FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kna\|1kna]], [[1kne\|1kne]], [[1q3l\|1q3l]], [[1pdq\|1pdq]], [[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kna\|1kna]], [[1kne\|1kne]], [[1q3l\|1q3l]], [[1pdq\|1pdq]], [[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]]</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=9606 ~~Homo sapiens~~])</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=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=2b2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b2y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2b2y RCSB], [http://www.ebi.ac.uk/pdbsum/2b2y 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=2b2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b2y OCA], [http://pdbe.org/2b2y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2b2y RCSB], [http://www.ebi.ac.uk/pdbsum/2b2y PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 2b2y" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Chruszcz, M]]		[[Category: Chruszcz, M]]
	[[Category: Clines, K L]]		[[Category: Clines, K L]]

OCA at 14:37, 25 December 2014

OCA — Thu, 25 Dec 2014 14:37:10 GMT

←Older revision		Revision as of 14:37, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2b2y]] is a 3 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=2B2Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2B2Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[2b2y]] is a 3 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=2B2Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2B2Y FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kna\|1kna]], [[1kne\|1kne]], [[1q3l\|1q3l]], [[1pdq\|1pdq]], [[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kna\|1kna]], [[1kne\|1kne]], [[1q3l\|1q3l]], [[1pdq\|1pdq]], [[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]]</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=9606 Homo sapiens])</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=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=2b2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b2y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2b2y RCSB], [http://www.ebi.ac.uk/pdbsum/2b2y 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=2b2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b2y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2b2y RCSB], [http://www.ebi.ac.uk/pdbsum/2b2y PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CHD1_HUMAN CHD1_HUMAN]] ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase 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. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Functions to modulate the efficiency of pre-mRNA splicing in part through physical bridging of spliceosomal components to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells.<ref>PMID:18042460</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Chruszcz, M.]]	+	[[Category: Chruszcz, M]]
-	[[Category: Clines, K L.]]	+	[[Category: Clines, K L]]
-	[[Category: Cymborowski, M.]]	+	[[Category: Cymborowski, M]]
-	[[Category: IV, J F.Flanagan.]]	+	[[Category: IV, J F.Flanagan]]
-	[[Category: Khorasanizadeh, S.]]	+	[[Category: Khorasanizadeh, S]]
-	[[Category: Kim, Y.]]	+	[[Category: Kim, Y]]
-	[[Category: Mi, L Z.]]	+	[[Category: Mi, L Z]]
-	[[Category: Minor, W.]]	+	[[Category: Minor, W]]
-	[[Category: Rastinejad, F.]]	+	[[Category: Rastinejad, F]]
	[[Category: Alpha helix linker]]		[[Category: Alpha helix linker]]
	[[Category: Chd]]		[[Category: Chd]]

OCA at 09:26, 29 September 2014

OCA — Mon, 29 Sep 2014 09:26:57 GMT

←Older revision		Revision as of 09:26, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2b2y.~~png~~\|~~left~~\|200px]]	+	==Tandem chromodomains of human CHD1==
		+	<StructureSection load='2b2y' size='340' side='right' caption='[[2b2y]], [[Resolution\|resolution]] 2.35Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2b2y]] is a 3 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=2B2Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2B2Y FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kna\|1kna]], [[1kne\|1kne]], [[1q3l\|1q3l]], [[1pdq\|1pdq]], [[2b2t\|2b2t]], [[2b2u\|2b2u]], [[2b2v\|2b2v]], [[2b2w\|2b2w]]</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=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=2b2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b2y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2b2y RCSB], [http://www.ebi.ac.uk/pdbsum/2b2y 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/b2/2b2y_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 ==
		+	Chromodomains are modules implicated in the recognition of lysine-methylated histone tails and nucleic acids. CHD (for chromo-ATPase/helicase-DNA-binding) proteins regulate ATP-dependent nucleosome assembly and mobilization through their conserved double chromodomains and SWI2/SNF2 helicase/ATPase domain. The Drosophila CHD1 localizes to the interbands and puffs of the polytene chromosomes, which are classic sites of transcriptional activity. Other CHD isoforms (CHD3/4 or Mi-2) are important for nucleosome remodelling in histone deacetylase complexes. Deletion of chromodomains impairs nucleosome binding and remodelling by CHD proteins. Here we describe the structure of the tandem arrangement of the human CHD1 chromodomains, and its interactions with histone tails. Unlike HP1 and Polycomb proteins that use single chromodomains to bind to their respective methylated histone H3 tails, the two chromodomains of CHD1 cooperate to interact with one methylated H3 tail. We show that the human CHD1 double chromodomains target the lysine 4-methylated histone H3 tail (H3K4me), a hallmark of active chromatin. Methylammonium recognition involves two aromatic residues, not the three-residue aromatic cage used by chromodomains of HP1 and Polycomb proteins. Furthermore, unique inserts within chromodomain 1 of CHD1 block the expected site of H3 tail binding seen in HP1 and Polycomb, instead directing H3 binding to a groove at the inter-chromodomain junction.

-	~~{{STRUCTURE_2b2y\| PDB=2b2y \| SCENE= }}~~	+	Double chromodomains cooperate to recognize the methylated histone H3 tail.,Flanagan JF, Mi LZ, Chruszcz M, Cymborowski M, Clines KL, Kim Y, Minor W, Rastinejad F, Khorasanizadeh S Nature. 2005 Dec 22;438(7071):1181-5. PMID:16372014<ref>PMID:16372014</ref>

-	~~===Tandem chromodomains~~ of ~~human CHD1===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16372014}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2b2y]] is a 3 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=2B2Y OCA].~~	+

	==See Also==		==See Also==
	*[[Chromodomain-helicase-DNA-binding protein\|Chromodomain-helicase-DNA-binding protein]]		*[[Chromodomain-helicase-DNA-binding protein\|Chromodomain-helicase-DNA-binding protein]]
-		+	*[[Helicase\|Helicase]]
-	==~~Reference~~==	+	== References ==
-	<~~ref group="xtra">PMID:016372014<~~/~~ref~~><~~references group="xtra"~~/>	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Chruszcz, M.]]		[[Category: Chruszcz, M.]]

OCA at 17:54, 20 October 2012

OCA — Sat, 20 Oct 2012 17:54:06 GMT

←Older revision		Revision as of 17:54, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2b2y]] is a 3 chain structure ~~of [[Chromodomain-helicase-DNA-binding protein]]~~ 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=2B2Y OCA].	+	[[2b2y]] is a 3 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=2B2Y OCA].

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

OCA: Protected "2b2y" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 02:21:39 GMT

Protected "2b2y" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:21, 27 July 2012

OCA at 02:21, 27 July 2012

OCA — Fri, 27 Jul 2012 02:21:37 GMT

←Older revision		Revision as of 02:21, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2b2y.png\|left\|200px]]		[[Image:2b2y.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2b2y", 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_2b2y\| PDB=2b2y \| SCENE= }}		{{STRUCTURE_2b2y\| PDB=2b2y \| SCENE= }}

	===Tandem chromodomains of human CHD1===		===Tandem chromodomains of human CHD1===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16372014}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16372014 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16372014}}		{{ABSTRACT_PUBMED_16372014}}

	==About this Structure==		==About this Structure==
-	~~2B2Y~~ is a 3 ~~chains~~ structure of ~~sequences~~ 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=2B2Y OCA].	+	[[2b2y]] is a 3 chain structure of [[Chromodomain-helicase-DNA-binding protein]] 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=2B2Y OCA].
		+
		+	==See Also==
		+	*[[Chromodomain-helicase-DNA-binding protein\|Chromodomain-helicase-DNA-binding protein]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16372014~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016372014</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Chruszcz, M.]]		[[Category: Chruszcz, M.]]
Line 37:		Line 28:
	[[Category: Chd]]		[[Category: Chd]]
	[[Category: Chromodomain]]		[[Category: Chromodomain]]
		+	[[Category: Peptide binding protein]]
	[[Category: Three stranded antiparallel beta sheet]]		[[Category: Three stranded antiparallel beta sheet]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:53:05 2009''

OCA at 16:53, 17 February 2009

OCA — Tue, 17 Feb 2009 16:53:06 GMT

←Older revision		Revision as of 16:53, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2B2Y is a ~~[[Protein complex]]~~ structure of sequences 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=2B2Y OCA].	+	2B2Y is a 3 chains structure of sequences 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=2B2Y OCA].

	==Reference==		==Reference==
-	Double chromodomains cooperate to recognize the methylated histone H3 tail., Flanagan JF, Mi LZ, Chruszcz M, Cymborowski M, Clines KL, Kim Y, Minor W, Rastinejad F, Khorasanizadeh S, Nature. 2005 Dec 22;438(7071):1181-5. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16372014 16372014]~~	+	<ref group="xtra">PMID:16372014</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Protein complex]]
	[[Category: Chruszcz, M.]]		[[Category: Chruszcz, M.]]
	[[Category: Clines, K L.]]		[[Category: Clines, K L.]]
Line 40:		Line 39:
	[[Category: Three stranded antiparallel beta sheet]]		[[Category: Three stranded antiparallel beta sheet]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 02~~:56:~~40 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:53:05 2009''