2dvs - Revision history

OCA at 00:52, 21 November 2024

2024-11-21T00:52:46Z

← Older revision		Revision as of 00:52, 21 November 2024
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dv/2dvs_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dv/2dvs_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=2dvs 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=2dvs ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Recognition of acetylated chromatin by the bromodomains and extra-terminal domain (BET) family proteins is a hallmark for transcriptional activation and anchoring viral genomes to mitotic chromosomes of the host. One of the BET family proteins BRD2 interacts with acetylated chromatin during mitosis and leads to transcriptional activation in culture cells. Here, we report the crystal structures of the N-terminal bromodomain of human BRD2 (BRD2-BD1; residues 74-194) in complex with each of three different Lys-12-acetylated H4 peptides. The BRD2-BD1 recognizes the H4 tail acetylated at Lys-12 (H4K12ac), whereas the side chain of hypoacetylated Lys-8 of H4 binds at the cavity of the dimer interface of BRD2-BD1. From binding studies, we identified the BRD2-BD1 residues that are responsible for recognition of the Lys-12-acetylated H4 tail. In addition, mutation to Lys-8 in the Lys-12-acetylated H4 tail decreased the binding to BRD2-BD1, implicating the critical role of Lys-8 in the Lys-12-acetylated H4 tail for the recognition by BRD2-BD1. Our findings provide a structural basis for deciphering the histone code by the BET bromodomain through the binding with a long segment of the histone H4 tail, which presumably prevents erasure of the histone code during the cell cycle.

			Structural basis for acetylated histone H4 recognition by the human BRD2 bromodomain.,Umehara T, Nakamura Y, Jang MK, Nakano K, Tanaka A, Ozato K, Padmanabhan B, Yokoyama S J Biol Chem. 2010 Mar 5;285(10):7610-8. Epub 2010 Jan 4. PMID:20048151<ref>PMID:20048151</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 2dvs" style="background-color:#fffaf0;"></div>

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

OCA at 06:25, 3 April 2024

2024-04-03T06:25:06Z

← Older revision		Revision as of 06:25, 3 April 2024
Line 3:		Line 3:
	<StructureSection load='2dvs' size='340' side='right'caption='[[2dvs]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='2dvs' size='340' side='right'caption='[[2dvs]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dvs]] is a 5 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=2DVS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DVS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dvs]] is a 5 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=2DVS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DVS FirstGlance]. <br>
	</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>~~, ~~<scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>~~</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]] 2.04Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height~~: ~~3em;~~'>~~[[1x0j\|1x0j]], [[2dvq\|2dvq]], [[2dvr\|2dvr]]~~</~~div~~></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=MSE:SELENOMETHIONINE'>MSE</scene></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=2dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dvs OCA], [https://pdbe.org/2dvs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dvs RCSB], [https://www.ebi.ac.uk/pdbsum/2dvs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dvs ProSAT], [https://www.topsan.org/Proteins/RSGI/2dvs TOPSAN]</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=2dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dvs OCA], [https://pdbe.org/2dvs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dvs RCSB], [https://www.ebi.ac.uk/pdbsum/2dvs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dvs ProSAT], [https://www.topsan.org/Proteins/RSGI/2dvs TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/BRD2_HUMAN BRD2_HUMAN]] May play a role in spermatogenesis or folliculogenesis (By similarity). Binds hyperacetylated chromatin and plays a role in the regulation of transcription, probably by chromatin remodeling. Regulates transcription of the CCND1 gene. Plays a role in nucleosome assembly.<ref>PMID:18406326</ref>		[https://www.uniprot.org/uniprot/BRD2_HUMAN BRD2_HUMAN] May play a role in spermatogenesis or folliculogenesis (By similarity). Binds hyperacetylated chromatin and plays a role in the regulation of transcription, probably by chromatin remodeling. Regulates transcription of the CCND1 gene. Plays a role in nucleosome assembly.<ref>PMID:18406326</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</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=2dvs 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=2dvs ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Recognition of acetylated chromatin by the bromodomains and extra-terminal domain (BET) family proteins is a hallmark for transcriptional activation and anchoring viral genomes to mitotic chromosomes of the host. One of the BET family proteins BRD2 interacts with acetylated chromatin during mitosis and leads to transcriptional activation in culture cells. Here, we report the crystal structures of the N-terminal bromodomain of human BRD2 (BRD2-BD1; residues 74-194) in complex with each of three different Lys-12-acetylated H4 peptides. The BRD2-BD1 recognizes the H4 tail acetylated at Lys-12 (H4K12ac), whereas the side chain of hypoacetylated Lys-8 of H4 binds at the cavity of the dimer interface of BRD2-BD1. From binding studies, we identified the BRD2-BD1 residues that are responsible for recognition of the Lys-12-acetylated H4 tail. In addition, mutation to Lys-8 in the Lys-12-acetylated H4 tail decreased the binding to BRD2-BD1, implicating the critical role of Lys-8 in the Lys-12-acetylated H4 tail for the recognition by BRD2-BD1. Our findings provide a structural basis for deciphering the histone code by the BET bromodomain through the binding with a long segment of the histone H4 tail, which presumably prevents erasure of the histone code during the cell cycle.

	Structural basis for acetylated histone H4 recognition by the human BRD2 bromodomain.,Umehara T, Nakamura Y, Jang MK, Nakano K, Tanaka A, Ozato K, Padmanabhan B, Yokoyama S J Biol Chem. 2010 Mar 5;285(10):7610-8. Epub 2010 Jan 4. PMID:20048151<ref>PMID:20048151</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2dvs" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
Line 36:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Nakamura, Y]]		[[Category: Nakamura Y]]
	[[Category: Padmanabhan, B]]		[[Category: Padmanabhan B]]
	~~[[Category: Structural genomic~~]]		[[Category: Shirouzu M]]
	[[Category: Shirouzu, M]]		[[Category: Umehara T]]
	[[Category: Umehara, T]]		[[Category: Yokoyama S]]
	[[Category: Yokoyama, S]]
	~~[[Category: Alpha-helical domain]]~~
	~~[[Category: Binds to acetylated histone]]~~
	~~[[Category: Bromodomain]]~~
	~~[[Category: National project on protein structural and functional analyse]]~~
	~~[[Category: Nppsfa]]~~
	~~[[Category: Rsgi]]~~
	~~[[Category: Transcription~~]]

OCA at 17:17, 15 December 2021

2021-12-15T17:17:23Z

← Older revision		Revision as of 17:17, 15 December 2021
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	<StructureSection load='2dvs' size='340' side='right'caption='[[2dvs]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='2dvs' size='340' side='right'caption='[[2dvs]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dvs]] is a 5 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=2DVS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DVS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dvs]] is a 5 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=2DVS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DVS FirstGlance]. <br>
	</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>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</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>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x0j\|1x0j]], [[2dvq\|2dvq]], [[2dvr\|2dvr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1x0j\|1x0j]], [[2dvq\|2dvq]], [[2dvr\|2dvr]]</div></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=2dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dvs OCA], [~~http~~://pdbe.org/2dvs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dvs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dvs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dvs ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/2dvs TOPSAN]</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=2dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dvs OCA], [https://pdbe.org/2dvs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dvs RCSB], [https://www.ebi.ac.uk/pdbsum/2dvs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dvs ProSAT], [https://www.topsan.org/Proteins/RSGI/2dvs TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/BRD2_HUMAN BRD2_HUMAN]] May play a role in spermatogenesis or folliculogenesis (By similarity). Binds hyperacetylated chromatin and plays a role in the regulation of transcription, probably by chromatin remodeling. Regulates transcription of the CCND1 gene. Plays a role in nucleosome assembly.<ref>PMID:18406326</ref>		[[https://www.uniprot.org/uniprot/BRD2_HUMAN BRD2_HUMAN]] May play a role in spermatogenesis or folliculogenesis (By similarity). Binds hyperacetylated chromatin and plays a role in the regulation of transcription, probably by chromatin remodeling. Regulates transcription of the CCND1 gene. Plays a role in nucleosome assembly.<ref>PMID:18406326</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:22, 11 March 2020

2020-03-11T08:22:00Z

← Older revision		Revision as of 08:22, 11 March 2020
Line 1:		Line 1:

	==Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with acetylated histone H4 peptide==		==Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with acetylated histone H4 peptide==
	<StructureSection load='2dvs' size='340' side='right' caption='[[2dvs]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='2dvs' size='340' side='right'caption='[[2dvs]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dvs]] is a 5 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=2DVS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DVS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dvs]] is a 5 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=2DVS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DVS FirstGlance]. <br>
Line 31:		Line 31:

	==See Also==		==See Also==
	*[[Bromodomain-containing protein\|Bromodomain-containing protein]]		*[[Bromodomain-containing protein 3D structures\|Bromodomain-containing protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Nakamura, Y]]		[[Category: Nakamura, Y]]
	[[Category: Padmanabhan, B]]		[[Category: Padmanabhan, B]]

OCA at 06:56, 6 June 2018

2018-06-06T06:56:30Z

← Older revision		Revision as of 06:56, 6 June 2018
Line 1:		Line 1:

	==Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with acetylated histone H4 peptide==		==Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with acetylated histone H4 peptide==
	<StructureSection load='2dvs' size='340' side='right' caption='[[2dvs]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='2dvs' size='340' side='right' caption='[[2dvs]], [[Resolution\|resolution]] 2.04Å' scene=''>
Line 5:		Line 6:
	</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>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</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>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x0j\|1x0j]], [[2dvq\|2dvq]], [[2dvr\|2dvr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x0j\|1x0j]], [[2dvq\|2dvq]], [[2dvr\|2dvr]]</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=2dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dvs OCA], [http://pdbe.org/2dvs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dvs RCSB], [http://www.ebi.ac.uk/pdbsum/2dvs PDBsum], [http://www.topsan.org/Proteins/RSGI/2dvs TOPSAN]</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=2dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dvs OCA], [http://pdbe.org/2dvs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dvs RCSB], [http://www.ebi.ac.uk/pdbsum/2dvs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dvs ProSAT], [http://www.topsan.org/Proteins/RSGI/2dvs TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dv/2dvs_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dv/2dvs_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 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2dvs" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2dvs" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Bromodomain-containing protein\|Bromodomain-containing protein]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 01:02, 8 February 2016

2016-02-08T01:02:07Z

← Older revision		Revision as of 01:02, 8 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=2dvs ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:25, 10 September 2015

2015-09-10T06:25:37Z

← Older revision		Revision as of 06:25, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2dvs' size='340' side='right' caption='[[2dvs]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='2dvs' size='340' side='right' caption='[[2dvs]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dvs]] is a 5 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=2DVS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DVS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dvs]] is a 5 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=2DVS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DVS FirstGlance]. <br>
	</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>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</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>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x0j\|1x0j]], [[2dvq\|2dvq]], [[2dvr\|2dvr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x0j\|1x0j]], [[2dvq\|2dvq]], [[2dvr\|2dvr]]</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=2dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dvs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dvs RCSB], [http://www.ebi.ac.uk/pdbsum/2dvs PDBsum], [http://www.topsan.org/Proteins/RSGI/2dvs TOPSAN]</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=2dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dvs OCA], [http://pdbe.org/2dvs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dvs RCSB], [http://www.ebi.ac.uk/pdbsum/2dvs PDBsum], [http://www.topsan.org/Proteins/RSGI/2dvs TOPSAN]</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 2dvs" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Homo sapiens~~]]		[[Category: Human]]
	[[Category: Nakamura, Y]]		[[Category: Nakamura, Y]]
	[[Category: Padmanabhan, B]]		[[Category: Padmanabhan, B]]

OCA at 19:26, 24 December 2014

2014-12-24T19:26:03Z

← Older revision		Revision as of 19:26, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dvs]] is a 5 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=2DVS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DVS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dvs]] is a 5 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=2DVS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DVS FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</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>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x0j\|1x0j]], [[2dvq\|2dvq]], [[2dvr\|2dvr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x0j\|1x0j]], [[2dvq\|2dvq]], [[2dvr\|2dvr]]</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=2dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dvs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dvs RCSB], [http://www.ebi.ac.uk/pdbsum/2dvs PDBsum], [http://www.topsan.org/Proteins/RSGI/2dvs TOPSAN]</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=2dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dvs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dvs RCSB], [http://www.ebi.ac.uk/pdbsum/2dvs PDBsum], [http://www.topsan.org/Proteins/RSGI/2dvs TOPSAN]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/BRD2_HUMAN BRD2_HUMAN]] May play a role in spermatogenesis or folliculogenesis (By similarity). Binds hyperacetylated chromatin and plays a role in the regulation of transcription, probably by chromatin remodeling. Regulates transcription of the CCND1 gene. Plays a role in nucleosome assembly.<ref>PMID:18406326</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Nakamura, Y.]]		[[Category: Nakamura, Y]]
	[[Category: Padmanabhan, B.]]		[[Category: Padmanabhan, B]]
	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]		[[Category: Structural genomic]]
	[[Category: Shirouzu, M.]]		[[Category: Shirouzu, M]]
	[[Category: Umehara, T.]]		[[Category: Umehara, T]]
	[[Category: Yokoyama, S.]]		[[Category: Yokoyama, S]]
	[[Category: Alpha-helical domain]]		[[Category: Alpha-helical domain]]
	[[Category: Binds to acetylated histone]]		[[Category: Binds to acetylated histone]]
Line 41:		Line 43:
	[[Category: National project on protein structural and functional analyse]]		[[Category: National project on protein structural and functional analyse]]
	[[Category: Nppsfa]]		[[Category: Nppsfa]]
	~~[[Category: Riken structural genomics/proteomics initiative]]~~
	[[Category: Rsgi]]		[[Category: Rsgi]]
	~~[[Category: Structural genomic]]~~
	[[Category: Transcription]]		[[Category: Transcription]]

OCA at 02:45, 30 September 2014

2014-09-30T02:45:49Z

← Older revision		Revision as of 02:45, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2dvs~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with acetylated histone H4 peptide==
			<StructureSection load='2dvs' size='340' side='right' caption='[[2dvs]], [[Resolution\|resolution]] 2.04Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2dvs]] is a 5 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=2DVS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DVS FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x0j\|1x0j]], [[2dvq\|2dvq]], [[2dvr\|2dvr]]</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=2dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dvs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dvs RCSB], [http://www.ebi.ac.uk/pdbsum/2dvs PDBsum], [http://www.topsan.org/Proteins/RSGI/2dvs TOPSAN]</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/dv/2dvs_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 ==
			Recognition of acetylated chromatin by the bromodomains and extra-terminal domain (BET) family proteins is a hallmark for transcriptional activation and anchoring viral genomes to mitotic chromosomes of the host. One of the BET family proteins BRD2 interacts with acetylated chromatin during mitosis and leads to transcriptional activation in culture cells. Here, we report the crystal structures of the N-terminal bromodomain of human BRD2 (BRD2-BD1; residues 74-194) in complex with each of three different Lys-12-acetylated H4 peptides. The BRD2-BD1 recognizes the H4 tail acetylated at Lys-12 (H4K12ac), whereas the side chain of hypoacetylated Lys-8 of H4 binds at the cavity of the dimer interface of BRD2-BD1. From binding studies, we identified the BRD2-BD1 residues that are responsible for recognition of the Lys-12-acetylated H4 tail. In addition, mutation to Lys-8 in the Lys-12-acetylated H4 tail decreased the binding to BRD2-BD1, implicating the critical role of Lys-8 in the Lys-12-acetylated H4 tail for the recognition by BRD2-BD1. Our findings provide a structural basis for deciphering the histone code by the BET bromodomain through the binding with a long segment of the histone H4 tail, which presumably prevents erasure of the histone code during the cell cycle.

	~~{{STRUCTURE_2dvs\| PDB=2dvs \| SCENE= }}~~		Structural basis for acetylated histone H4 recognition by the human BRD2 bromodomain.,Umehara T, Nakamura Y, Jang MK, Nakano K, Tanaka A, Ozato K, Padmanabhan B, Yokoyama S J Biol Chem. 2010 Mar 5;285(10):7610-8. Epub 2010 Jan 4. PMID:20048151<ref>PMID:20048151</ref>

	~~===Crystal structure analysis~~ of the ~~N-terminal bromodomain of human BRD2 complexed with acetylated histone H4 peptide===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_20048151}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2dvs]] is a 5 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=2DVS OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:020048151<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Nakamura, Y.]]		[[Category: Nakamura, Y.]]

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

2013-01-06T11:57:42Z

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

← Older revision	Revision as of 11:57, 6 January 2013
(No difference)