2h9u - Revision history

OCA at 08:50, 25 October 2023

OCA — Wed, 25 Oct 2023 08:50:26 GMT

←Older revision		Revision as of 08:50, 25 October 2023
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	<StructureSection load='2h9u' size='340' side='right'caption='[[2h9u]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2h9u' size='340' side='right'caption='[[2h9u]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2h9u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Aerpe Aerpe~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H9U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2h9u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix_K1 Aeropyrum pernix K1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H9U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=2h9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9u OCA], [https://pdbe.org/2h9u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h9u RCSB], [https://www.ebi.ac.uk/pdbsum/2h9u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h9u ProSAT], [https://www.topsan.org/Proteins/RSGI/2h9u 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=2h9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9u OCA], [https://pdbe.org/2h9u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h9u RCSB], [https://www.ebi.ac.uk/pdbsum/2h9u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h9u ProSAT], [https://www.topsan.org/Proteins/RSGI/2h9u TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/ALBA2_AERPE ALBA2_AERPE]] Binds double-stranded DNA tightly but without sequence specificity. It is distributed uniformly and abundantly on the chromosome, suggesting a role in chromatin architecture. However, it does not significantly compact DNA. Binds rRNA and mRNA in vivo. May play a role in maintaining the structural and functional stability of RNA, and, perhaps, ribosomes (By similarity).	+	[https://www.uniprot.org/uniprot/ALBA2_AERPE ALBA2_AERPE] Binds double-stranded DNA tightly but without sequence specificity. It is distributed uniformly and abundantly on the chromosome, suggesting a role in chromatin architecture. However, it does not significantly compact DNA. Binds rRNA and mRNA in vivo. May play a role in maintaining the structural and functional stability of RNA, and, perhaps, ribosomes (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=2h9u 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=2h9u ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Eukaryotic DNA is packaged into nucleosomes that regulate the accessibility of the genome to replication, transcription and repair factors. Chromatin accessibility is controlled by histone modifications including acetylation and methylation. Archaea possess eukary otic-like machineries for DNA replication, transcription and information processing. The conserved archaeal DNA binding protein Alba (formerly Sso10b) interacts with the silencing protein Sir2, which regulates Alba's DNA binding affinity by deacetylation of a lysine residue. We present the crystal structure of Alba from Sulfolobus solfataricus at 2.6 A resolution (PDB code 1h0x). The fold is reminiscent of the N-terminal DNA binding domain of DNase I and the C-terminal domain of initiation factor IF3. The Alba dimer has two extended beta-hairpins flanking a central body containing the acetylated lysine, Lys16, suggesting three main points of contact with the DNA. Fluorescence, calorimetry and electrophoresis data suggest a final binding stoichiometry of approximately 5 bp DNA per Alba dimer. We present a model for the Alba-DNA interaction consistent with the available structural, biophysical and electron microscopy data.
-
-	Structure of Alba: an archaeal chromatin protein modulated by acetylation.,Wardleworth BN, Russell RJ, Bell SD, Taylor GL, White MF EMBO J. 2002 Sep 2;21(17):4654-62. PMID:12198167<ref>PMID:12198167</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2h9u" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aerpe~~]]	+	[[Category: Aeropyrum pernix K1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kumarevel~~, T S]]~~	+	[[Category: Kumarevel TS]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Sakamoto K]]
-	[[Category: Sakamoto, K]]	+	[[Category: Shinkai A]]
-	[[Category: Shinkai, A]]	+	[[Category: Yokoyama S]]
-	[[Category: Yokoyama, S]]	+
-	~~[[Category: Aeropyrum pernix]]~~	+
-	~~[[Category: Archaea]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: National project on protein structural and functional analyse]]~~	+
-	~~[[Category: Nppsfa]]~~	+
-	~~[[Category: Rsgi~~]]	+

OCA at 10:03, 12 May 2021

OCA — Wed, 12 May 2021 10:03:01 GMT

←Older revision		Revision as of 10:03, 12 May 2021
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	<StructureSection load='2h9u' size='340' side='right'caption='[[2h9u]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2h9u' size='340' side='right'caption='[[2h9u]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2h9u]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2H9U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2h9u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H9U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></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=2h9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9u OCA], [~~http~~://pdbe.org/2h9u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2h9u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2h9u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2h9u ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/2h9u 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=2h9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9u OCA], [https://pdbe.org/2h9u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h9u RCSB], [https://www.ebi.ac.uk/pdbsum/2h9u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h9u ProSAT], [https://www.topsan.org/Proteins/RSGI/2h9u TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ALBA2_AERPE ALBA2_AERPE]] Binds double-stranded DNA tightly but without sequence specificity. It is distributed uniformly and abundantly on the chromosome, suggesting a role in chromatin architecture. However, it does not significantly compact DNA. Binds rRNA and mRNA in vivo. May play a role in maintaining the structural and functional stability of RNA, and, perhaps, ribosomes (By similarity).	+	[[https://www.uniprot.org/uniprot/ALBA2_AERPE ALBA2_AERPE]] Binds double-stranded DNA tightly but without sequence specificity. It is distributed uniformly and abundantly on the chromosome, suggesting a role in chromatin architecture. However, it does not significantly compact DNA. Binds rRNA and mRNA in vivo. May play a role in maintaining the structural and functional stability of RNA, and, perhaps, ribosomes (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:15, 24 July 2019

OCA — Wed, 24 Jul 2019 09:15:48 GMT

←Older revision		Revision as of 09:15, 24 July 2019
Line 1:		Line 1:

	==Crystal structure of the archaea specific DNA binding protein==		==Crystal structure of the archaea specific DNA binding protein==
-	<StructureSection load='2h9u' size='340' side='right' caption='[[2h9u]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='2h9u' size='340' side='right'caption='[[2h9u]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2h9u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H9U FirstGlance]. <br>		<table><tr><td colspan='2'>[[2h9u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H9U FirstGlance]. <br>
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h9/2h9u_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h9/2h9u_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 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Aerpe]]		[[Category: Aerpe]]
		+	[[Category: Large Structures]]
	[[Category: Kumarevel, T S]]		[[Category: Kumarevel, T S]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 08:08, 18 October 2017

OCA — Wed, 18 Oct 2017 08:08:50 GMT

←Older revision		Revision as of 08:08, 18 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of the archaea specific DNA binding protein==		==Crystal structure of the archaea specific DNA binding protein==
	<StructureSection load='2h9u' size='340' side='right' caption='[[2h9u]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2h9u' size='340' side='right' caption='[[2h9u]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2h9u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H9U FirstGlance]. <br>		<table><tr><td colspan='2'>[[2h9u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H9U FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></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=2h9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9u OCA], [http://pdbe.org/2h9u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2h9u RCSB], [http://www.ebi.ac.uk/pdbsum/2h9u PDBsum], [http://www.topsan.org/Proteins/RSGI/2h9u 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=2h9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9u OCA], [http://pdbe.org/2h9u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2h9u RCSB], [http://www.ebi.ac.uk/pdbsum/2h9u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2h9u ProSAT], [http://www.topsan.org/Proteins/RSGI/2h9u TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		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=2h9u ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:47, 11 September 2015

OCA — Fri, 11 Sep 2015 13:47:43 GMT

←Older revision		Revision as of 13:47, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2h9u' size='340' side='right' caption='[[2h9u]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2h9u' size='340' side='right' caption='[[2h9u]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2h9u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Aeropyrum_pernix Aeropyrum pernix~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H9U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2h9u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H9U FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></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=2h9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2h9u RCSB], [http://www.ebi.ac.uk/pdbsum/2h9u PDBsum], [http://www.topsan.org/Proteins/RSGI/2h9u 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=2h9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9u OCA], [http://pdbe.org/2h9u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2h9u RCSB], [http://www.ebi.ac.uk/pdbsum/2h9u PDBsum], [http://www.topsan.org/Proteins/RSGI/2h9u TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	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 2h9u" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aeropyrum pernix~~]]	+	[[Category: Aerpe]]
	[[Category: Kumarevel, T S]]		[[Category: Kumarevel, T S]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
Line 36:		Line 37:
	[[Category: Shinkai, A]]		[[Category: Shinkai, A]]
	[[Category: Yokoyama, S]]		[[Category: Yokoyama, S]]
		+	[[Category: Aeropyrum pernix]]
	[[Category: Archaea]]		[[Category: Archaea]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]

OCA at 17:16, 25 December 2014

OCA — Thu, 25 Dec 2014 17:16:52 GMT

←Older revision		Revision as of 17:16, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2h9u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H9U FirstGlance]. <br>		<table><tr><td colspan='2'>[[2h9u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H9U FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></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=2h9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2h9u RCSB], [http://www.ebi.ac.uk/pdbsum/2h9u PDBsum], [http://www.topsan.org/Proteins/RSGI/2h9u 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=2h9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2h9u RCSB], [http://www.ebi.ac.uk/pdbsum/2h9u PDBsum], [http://www.topsan.org/Proteins/RSGI/2h9u TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ALBA2_AERPE ALBA2_AERPE]] Binds double-stranded DNA tightly but without sequence specificity. It is distributed uniformly and abundantly on the chromosome, suggesting a role in chromatin architecture. However, it does not significantly compact DNA. Binds rRNA and mRNA in vivo. May play a role in maintaining the structural and functional stability of RNA, and, perhaps, ribosomes (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Aeropyrum pernix]]		[[Category: Aeropyrum pernix]]
-	[[Category: Kumarevel, T S.]]	+	[[Category: Kumarevel, T S]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Sakamoto, K.]]	+	[[Category: Sakamoto, K]]
-	[[Category: Shinkai, A.]]	+	[[Category: Shinkai, A]]
-	[[Category: Yokoyama, S~~.]]~~	+	[[Category: Yokoyama, S]]
-	~~[[Category: Aeropyrum pernix~~]]	+
	[[Category: Archaea]]		[[Category: Archaea]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[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]]

OCA at 07:59, 30 September 2014

OCA — Tue, 30 Sep 2014 07:59:35 GMT

←Older revision		Revision as of 07:59, 30 September 2014
Line 1:		Line 1:
-	[[~~Image~~:2h9u.~~png\|left~~\|200px]]	+	==Crystal structure of the archaea specific DNA binding protein==
		+	<StructureSection load='2h9u' size='340' side='right' caption='[[2h9u]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2h9u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H9U FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene><br>
		+	<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=2h9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2h9u RCSB], [http://www.ebi.ac.uk/pdbsum/2h9u PDBsum], [http://www.topsan.org/Proteins/RSGI/2h9u 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/h9/2h9u_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 ==
		+	Eukaryotic DNA is packaged into nucleosomes that regulate the accessibility of the genome to replication, transcription and repair factors. Chromatin accessibility is controlled by histone modifications including acetylation and methylation. Archaea possess eukary otic-like machineries for DNA replication, transcription and information processing. The conserved archaeal DNA binding protein Alba (formerly Sso10b) interacts with the silencing protein Sir2, which regulates Alba's DNA binding affinity by deacetylation of a lysine residue. We present the crystal structure of Alba from Sulfolobus solfataricus at 2.6 A resolution (PDB code 1h0x). The fold is reminiscent of the N-terminal DNA binding domain of DNase I and the C-terminal domain of initiation factor IF3. The Alba dimer has two extended beta-hairpins flanking a central body containing the acetylated lysine, Lys16, suggesting three main points of contact with the DNA. Fluorescence, calorimetry and electrophoresis data suggest a final binding stoichiometry of approximately 5 bp DNA per Alba dimer. We present a model for the Alba-DNA interaction consistent with the available structural, biophysical and electron microscopy data.

-	~~{{STRUCTURE_2h9u\| PDB=2h9u \| SCENE= }}~~	+	Structure of Alba: an archaeal chromatin protein modulated by acetylation.,Wardleworth BN, Russell RJ, Bell SD, Taylor GL, White MF EMBO J. 2002 Sep 2;21(17):4654-62. PMID:12198167<ref>PMID:12198167</ref>

-	~~===Crystal structure~~ of the ~~archaea specific DNA binding protein===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12198167}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2h9u]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Aeropyrum_pernix Aeropyrum pernix]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2H9U OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012198167<~~/~~ref~~><~~ref group="xtra">PMID:018004791</ref><references group="xtra"~~/>	+
	[[Category: Aeropyrum pernix]]		[[Category: Aeropyrum pernix]]
	[[Category: Kumarevel, T S.]]		[[Category: Kumarevel, T S.]]

OCA: Protected "2h9u" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 13:05:09 GMT

Protected "2h9u" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:05, 7 January 2013

OCA at 13:05, 7 January 2013

OCA — Mon, 07 Jan 2013 13:05:06 GMT

←Older revision		Revision as of 13:05, 7 January 2013
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-	{{Seed}}
	[[Image:2h9u.png\|left\|200px]]		[[Image:2h9u.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2h9u", 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_2h9u\| PDB=2h9u \| SCENE= }}		{{STRUCTURE_2h9u\| PDB=2h9u \| SCENE= }}

	===Crystal structure of the archaea specific DNA binding protein===		===Crystal structure of the archaea specific DNA binding protein===

		+	{{ABSTRACT_PUBMED_12198167}}

	==About this Structure==		==About this Structure==
-	~~2H9U~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9U OCA].	+	[[2h9u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9U OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12198167~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012198167</ref><ref group="xtra">PMID:018004791</ref><references group="xtra"/>
	[[Category: Aeropyrum pernix]]		[[Category: Aeropyrum pernix]]
	[[Category: Kumarevel, T S.]]		[[Category: Kumarevel, T S.]]
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	[[Category: Aeropyrum pernix]]		[[Category: Aeropyrum pernix]]
	[[Category: Archaea]]		[[Category: Archaea]]
-	[[Category: Crystal structure]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: National project on protein structural and functional analyse]]		[[Category: National project on protein structural and functional analyse]]
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	[[Category: Rsgi]]		[[Category: Rsgi]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 23:58:09 2009''

OCA at 21:58, 17 February 2009

OCA — Tue, 17 Feb 2009 21:58:10 GMT

←Older revision		Revision as of 21:58, 17 February 2009
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	===Crystal structure of the archaea specific DNA binding protein===		===Crystal structure of the archaea specific DNA binding protein===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12198167}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12198167 is the PubMed ID number.
-	-->
-	{{ABSTRACT_PUBMED_12198167}}

	==About this Structure==		==About this Structure==
Line 23:		Line 17:

	==Reference==		==Reference==
-	~~Structure of Alba: an archaeal chromatin protein modulated by acetylation., Wardleworth BN, Russell RJ, Bell SD, Taylor GL, White MF, EMBO J. 2002 Sep 2;21(17):4654-62.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/12198167 12198167]~~	+	<ref group="xtra">PMID:12198167</ref><references group="xtra"/>
	[[Category: Aeropyrum pernix]]		[[Category: Aeropyrum pernix]]
	[[Category: Kumarevel, T S.]]		[[Category: Kumarevel, T S.]]
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	[[Category: Structural genomic]]		[[Category: Structural genomic]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Nov 16 15~~:12:~~21 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 23:58:09 2009''