2kwj - Revision history

OCA at 08:34, 15 November 2023

OCA — Wed, 15 Nov 2023 08:34:12 GMT

←Older revision		Revision as of 08:34, 15 November 2023
Line 1:		Line 1:

	==Solution structures of the double PHD fingers of human transcriptional protein DPF3 bound to a histone peptide containing acetylation at lysine 14==		==Solution structures of the double PHD fingers of human transcriptional protein DPF3 bound to a histone peptide containing acetylation at lysine 14==
-	<StructureSection load='2kwj' size='340' side='right'caption='[[2kwj~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='2kwj' size='340' side='right'caption='[[2kwj]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2kwj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KWJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KWJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2kwj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KWJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KWJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[2kwk\|2kwk]], [[2kwn\|2kwn]], [[2kwo\|2kwo]]~~</~~div~~>~~</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DPF3, BAF45C, CERD4 ([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=2kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kwj OCA], [https://pdbe.org/2kwj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kwj RCSB], [https://www.ebi.ac.uk/pdbsum/2kwj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kwj 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=2kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kwj OCA], [https://pdbe.org/2kwj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kwj RCSB], [https://www.ebi.ac.uk/pdbsum/2kwj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kwj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~DPF3_HUMAN DPF3_HUMAN~~]] Belongs to the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). Muscle-specific component of the BAF complex, a multiprotein complex involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Specifically binds acetylated lysines on histone 3 and 4 (H3K14ac, H3K9ac, H4K5ac, H4K8ac, H4K12ac, H4K16ac). In the complex, it acts as a tissue-specific anchor between histone acetylations and methylations and chromatin remodeling. It thereby probably plays an essential role in heart and skeletal muscle development.<ref>PMID:18765789</ref>	+	[https://www.uniprot.org/uniprot/H31_HUMAN H31_HUMAN]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Li, S]]	+	[[Category: Li S]]
-	[[Category: Plotnikov~~, A N~~]]	+	[[Category: Plotnikov AN]]
-	[[Category: Walsh~~, M J~~]]	+	[[Category: Walsh MJ]]
-	[[Category: Zeng, L]]	+	[[Category: Zeng L]]
-	[[Category: Zhang, Q]]	+	[[Category: Zhang Q]]
-	[[Category: Zhou, M]]	+	[[Category: Zhou M]]
-	~~[[Category: Acetyl-lysine]]~~	+
-	~~[[Category: Metal binding protein]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Transcription regulation~~]]	+

OCA at 07:33, 14 April 2021

OCA — Wed, 14 Apr 2021 07:33:08 GMT

←Older revision		Revision as of 07:33, 14 April 2021
Line 1:		Line 1:

	==Solution structures of the double PHD fingers of human transcriptional protein DPF3 bound to a histone peptide containing acetylation at lysine 14==		==Solution structures of the double PHD fingers of human transcriptional protein DPF3 bound to a histone peptide containing acetylation at lysine 14==
-	<StructureSection load='2kwj' size='340' side='right' caption='[[2kwj]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='2kwj' size='340' side='right'caption='[[2kwj]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2kwj]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KWJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2KWJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2kwj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KWJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KWJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2kwk\|2kwk]], [[2kwn\|2kwn]], [[2kwo\|2kwo]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2kwk\|2kwk]], [[2kwn\|2kwn]], [[2kwo\|2kwo]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DPF3, BAF45C, CERD4 ([~~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">DPF3, BAF45C, CERD4 ([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=2kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kwj OCA], [~~http~~://pdbe.org/2kwj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2kwj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2kwj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2kwj 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=2kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kwj OCA], [https://pdbe.org/2kwj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kwj RCSB], [https://www.ebi.ac.uk/pdbsum/2kwj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kwj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DPF3_HUMAN DPF3_HUMAN]] Belongs to the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). Muscle-specific component of the BAF complex, a multiprotein complex involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Specifically binds acetylated lysines on histone 3 and 4 (H3K14ac, H3K9ac, H4K5ac, H4K8ac, H4K12ac, H4K16ac). In the complex, it acts as a tissue-specific anchor between histone acetylations and methylations and chromatin remodeling. It thereby probably plays an essential role in heart and skeletal muscle development.<ref>PMID:18765789</ref>	+	[[https://www.uniprot.org/uniprot/DPF3_HUMAN DPF3_HUMAN]] Belongs to the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). Muscle-specific component of the BAF complex, a multiprotein complex involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Specifically binds acetylated lysines on histone 3 and 4 (H3K14ac, H3K9ac, H4K5ac, H4K8ac, H4K12ac, H4K16ac). In the complex, it acts as a tissue-specific anchor between histone acetylations and methylations and chromatin remodeling. It thereby probably plays an essential role in heart and skeletal muscle development.<ref>PMID:18765789</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Li, S]]		[[Category: Li, S]]
	[[Category: Plotnikov, A N]]		[[Category: Plotnikov, A N]]

OCA at 08:29, 25 July 2018

OCA — Wed, 25 Jul 2018 08:29:04 GMT

←Older revision		Revision as of 08:29, 25 July 2018
Line 1:		Line 1:
		+
	==Solution structures of the double PHD fingers of human transcriptional protein DPF3 bound to a histone peptide containing acetylation at lysine 14==		==Solution structures of the double PHD fingers of human transcriptional protein DPF3 bound to a histone peptide containing acetylation at lysine 14==
	<StructureSection load='2kwj' size='340' side='right' caption='[[2kwj]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2kwj' size='340' side='right' caption='[[2kwj]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2kwk\|2kwk]], [[2kwn\|2kwn]], [[2kwo\|2kwo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2kwk\|2kwk]], [[2kwn\|2kwn]], [[2kwo\|2kwo]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DPF3, BAF45C, CERD4 ([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">DPF3, BAF45C, CERD4 ([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=2kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kwj OCA], [http://pdbe.org/2kwj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kwj RCSB], [http://www.ebi.ac.uk/pdbsum/2kwj 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=2kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kwj OCA], [http://pdbe.org/2kwj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kwj RCSB], [http://www.ebi.ac.uk/pdbsum/2kwj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2kwj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kw/2kwj_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kw/2kwj_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>
	</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=2kwj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:08, 10 September 2015

OCA — Thu, 10 Sep 2015 05:08:28 GMT

←Older revision		Revision as of 05:08, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2kwj' size='340' side='right' caption='[[2kwj]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2kwj' size='340' side='right' caption='[[2kwj]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2kwj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KWJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KWJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2kwj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KWJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KWJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2kwk\|2kwk]], [[2kwn\|2kwn]], [[2kwo\|2kwo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2kwk\|2kwk]], [[2kwn\|2kwn]], [[2kwo\|2kwo]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DPF3, BAF45C, CERD4 ([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">DPF3, BAF45C, CERD4 ([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=2kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kwj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kwj RCSB], [http://www.ebi.ac.uk/pdbsum/2kwj 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=2kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kwj OCA], [http://pdbe.org/2kwj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kwj RCSB], [http://www.ebi.ac.uk/pdbsum/2kwj PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 2kwj" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Li, S]]		[[Category: Li, S]]
	[[Category: Plotnikov, A N]]		[[Category: Plotnikov, A N]]

OCA at 18:22, 24 December 2014

OCA — Wed, 24 Dec 2014 18:22:42 GMT

←Older revision		Revision as of 18:22, 24 December 2014
Line 9:		Line 9:
	<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=2kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kwj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kwj RCSB], [http://www.ebi.ac.uk/pdbsum/2kwj 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=2kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kwj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kwj RCSB], [http://www.ebi.ac.uk/pdbsum/2kwj PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPF3_HUMAN DPF3_HUMAN]] Belongs to the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). Muscle-specific component of the BAF complex, a multiprotein complex involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Specifically binds acetylated lysines on histone 3 and 4 (H3K14ac, H3K9ac, H4K5ac, H4K8ac, H4K12ac, H4K16ac). In the complex, it acts as a tissue-specific anchor between histone acetylations and methylations and chromatin remodeling. It thereby probably plays an essential role in heart and skeletal muscle development.<ref>PMID:18765789</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 12:43, 18 December 2014

OCA — Thu, 18 Dec 2014 12:43:22 GMT

←Older revision		Revision as of 12:43, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2kwj\| PDB=2kwj \| SCENE= }}~~	+	==Solution structures of the double PHD fingers of human transcriptional protein DPF3 bound to a histone peptide containing acetylation at lysine 14==
-	===Solution structures of the double PHD fingers of human transcriptional protein DPF3 bound to a histone peptide containing acetylation at lysine 14===	+	<StructureSection load='2kwj' size='340' side='right' caption='[[2kwj]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
-	~~{{ABSTRACT_PUBMED_20613843}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2kwj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KWJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KWJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2kwk\|2kwk]], [[2kwn\|2kwn]], [[2kwo\|2kwo]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DPF3, BAF45C, CERD4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=2kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kwj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kwj RCSB], [http://www.ebi.ac.uk/pdbsum/2kwj 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/kw/2kwj_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 ==
		+	Histone lysine acetylation and methylation have an important role during gene transcription in a chromatin context. Knowledge concerning the types of protein modules that can interact with acetyl-lysine has so far been limited to bromodomains. Recently, a tandem plant homeodomain (PHD) finger (PHD1-PHD2, or PHD12) of human DPF3b, which functions in association with the BAF chromatin remodelling complex to initiate gene transcription during heart and muscle development, was reported to bind histones H3 and H4 in an acetylation-sensitive manner, making it the first alternative to bromodomains for acetyl-lysine binding. Here we report the structural mechanism of acetylated histone binding by the double PHD fingers of DPF3b. Our three-dimensional solution structures and biochemical analysis of DPF3b highlight the molecular basis of the integrated tandem PHD finger, which acts as one functional unit in the sequence-specific recognition of lysine-14-acetylated histone H3 (H3K14ac). Whereas the interaction with H3 is promoted by acetylation at lysine 14, it is inhibited by methylation at lysine 4, and these opposing influences are important during transcriptional activation of the mouse DPF3b target genes Pitx2 and Jmjd1c. Binding of this tandem protein module to chromatin can thus be regulated by different histone modifications during the initiation of gene transcription.

-	~~==Function==~~	+	Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b.,Zeng L, Zhang Q, Li S, Plotnikov AN, Walsh MJ, Zhou MM Nature. 2010 Jul 8;466(7303):258-62. PMID:20613843<ref>PMID:20613843</ref>
-	[[http://www.uniprot.org/uniprot/DPF3_HUMAN DPF3_HUMAN]] Belongs to the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and ~~become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition~~ of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of ~~the multipotent neural stem cells~~. ~~The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). Muscle-specific component of the BAF complex~~, a multiprotein complex involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Specifically binds acetylated lysines on histone 3 and 4 (H3K14ac, ~~H3K9ac~~, ~~H4K5ac~~, ~~H4K8ac~~, ~~H4K12ac~~, ~~H4K16ac~~)~~. In the complex, it acts as a tissue~~-~~specific anchor between histone acetylations and methylations and chromatin remodeling. It thereby probably plays an essential role in heart and skeletal muscle development~~.<ref>PMID:~~18765789~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[2kwj]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2KWJ OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:020613843</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Li, S.]]	+	[[Category: Li, S]]
-	[[Category: Plotnikov, A N.]]	+	[[Category: Plotnikov, A N]]
-	[[Category: Walsh, M J.]]	+	[[Category: Walsh, M J]]
-	[[Category: Zeng, L.]]	+	[[Category: Zeng, L]]
-	[[Category: Zhang, Q.]]	+	[[Category: Zhang, Q]]
-	[[Category: Zhou, M.]]	+	[[Category: Zhou, M]]
	[[Category: Acetyl-lysine]]		[[Category: Acetyl-lysine]]
	[[Category: Metal binding protein]]		[[Category: Metal binding protein]]
	[[Category: Nucleus]]		[[Category: Nucleus]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]

OCA at 09:21, 19 June 2013

OCA — Wed, 19 Jun 2013 09:21:19 GMT

←Older revision		Revision as of 09:21, 19 June 2013
Line 1:		Line 1:
-	[[Image:2kwj.png\|left\|200px]]
-
	{{STRUCTURE_2kwj\| PDB=2kwj \| SCENE= }}		{{STRUCTURE_2kwj\| PDB=2kwj \| SCENE= }}
-
	===Solution structures of the double PHD fingers of human transcriptional protein DPF3 bound to a histone peptide containing acetylation at lysine 14===		===Solution structures of the double PHD fingers of human transcriptional protein DPF3 bound to a histone peptide containing acetylation at lysine 14===
		+	{{ABSTRACT_PUBMED_20613843}}

-	~~{{ABSTRACT_PUBMED_020613843}}~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/DPF3_HUMAN DPF3_HUMAN]] Belongs to the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). Muscle-specific component of the BAF complex, a multiprotein complex involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Specifically binds acetylated lysines on histone 3 and 4 (H3K14ac, H3K9ac, H4K5ac, H4K8ac, H4K12ac, H4K16ac). In the complex, it acts as a tissue-specific anchor between histone acetylations and methylations and chromatin remodeling. It thereby probably plays an essential role in heart and skeletal muscle development.<ref>PMID:18765789</ref>

	==About this Structure==		==About this Structure==
	[[2kwj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KWJ OCA].		[[2kwj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KWJ OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:020613843</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Li, S.]]		[[Category: Li, S.]]

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

OCA — Mon, 07 Jan 2013 11:19:30 GMT

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

←Older revision

Revision as of 11:19, 7 January 2013

OCA at 11:19, 7 January 2013

OCA — Mon, 07 Jan 2013 11:19:26 GMT

←Older revision		Revision as of 11:19, 7 January 2013
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:2kwj.png\|left\|200px]]
-	[[Image:2kwj.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2kwj", 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_2kwj\| PDB=2kwj \| SCENE= }}		{{STRUCTURE_2kwj\| PDB=2kwj \| SCENE= }}

	===Solution structures of the double PHD fingers of human transcriptional protein DPF3 bound to a histone peptide containing acetylation at lysine 14===		===Solution structures of the double PHD fingers of human transcriptional protein DPF3 bound to a histone peptide containing acetylation at lysine 14===

		+	{{ABSTRACT_PUBMED_020613843}}

	==About this Structure==		==About this Structure==
-	~~2KWJ~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KWJ OCA].	+	[[2kwj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KWJ OCA].
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Li, S.]]		[[Category: Li, S.]]
Line 26:		Line 20:
	[[Category: Nucleus]]		[[Category: Nucleus]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 14 16:15:26 2010''

OCA at 12:09, 14 July 2010

OCA — Wed, 14 Jul 2010 12:09:18 GMT

←Older revision		Revision as of 12:09, 14 July 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:2kwj.jpg\|left\|200px]]

-	The ~~entry 2kwj~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_2kwj", 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_2kwj\| PDB=2kwj \| SCENE= }}

-	~~Authors: Zeng, L., Zhang, Q., Li, S., Plotnikov, A.N., Walsh, M.J., Zhou, M.~~	+	===Solution structures of the double PHD fingers of human transcriptional protein DPF3 bound to a histone peptide containing acetylation at lysine 14===

-	Description: Solution structures of the double PHD fingers of human transcriptional protein DPF3 bound to a histone peptide containing acetylation at lysine 14

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~May 5 11~~:31:23 2010''	+	==About this Structure==
		+	2KWJ is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KWJ OCA].
		+	[[Category: Homo sapiens]]
		+	[[Category: Li, S.]]
		+	[[Category: Plotnikov, A N.]]
		+	[[Category: Walsh, M J.]]
		+	[[Category: Zeng, L.]]
		+	[[Category: Zhang, Q.]]
		+	[[Category: Zhou, M.]]
		+	[[Category: Acetyl-lysine]]
		+	[[Category: Metal binding protein]]
		+	[[Category: Nucleus]]
		+	[[Category: Transcription regulation]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 14 16:15:26 2010''