1b6w - Revision history

OCA at 05:55, 3 April 2024

OCA — Wed, 03 Apr 2024 05:55:39 GMT

←Older revision		Revision as of 05:55, 3 April 2024
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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=1b6w 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=1b6w ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The hyperthermophilic archaeon Methanothermus fervidus contains two small basic proteins, HMfA (68 amino acid residues) and HMfB (69 residues) that share a common ancestry with the eukaryal nucleosome core histones H2A, H2B, H3, and H4. HMfA and HMfB have sequences that differ at 11 locations, they have different structural stabilities, and the complexes that they form with DNA have different electrophoretic mobilities. Here, crystal structures are documented for recombinant (r) HMfA at a resolution of 1.55 A refined to a crystallographic R-value of 19.8 % (tetragonal form) and at 1.48 A refined to a R-value of 18.8 % (orthorhombic form), and for rHMfB at 1.9 A refined to a R-value of 18.0 %. The rHMfA and rHMfB monomers have structures that are just histone folds in which a long central alpha-helix (alpha2; 29 residues) is separated from shorter N-terminal (alpha1; 11 residues) and C-terminal (alpha3; 10 residues) alpha-helices by two loops (L1 and L2; both 6 residues). Within L1 and L2, three adjacent residues are in extended (beta) conformation. rHMfA and rHMfB assemble into homodimers, with the alpha2 helices anti-parallel aligned and crossing at an angle of close to 35 degrees, and with hydrogen bonds formed between the extended, parallel regions of L1 and L2 resulting in short beta-ladders. Dimerization creates a novel N-terminal structure that contains four proline residues, two from each monomer. As prolines are present at these positions in all archaeal histone sequences, this proline-tetrad structure is likely to be a common feature of all archaeal histone dimers. Almost all residues that participate in monomer-monomer interactions are conserved in HMfA and HMfB, consistent with the ability of these monomers to form both homodimers and (HMfA+HMfB) heterodimers. Differences in side-chain interactions that result from non-conservative residue differences in HMfA and HMfB are identified, and the structure of a (rHMfA)(2)-DNA complex is presented based on the structures documented here and modeled by homology to histone-DNA interactions in the eukaryal nucleosome.
-
-	Crystal structures of recombinant histones HMfA and HMfB from the hyperthermophilic archaeon Methanothermus fervidus.,Decanniere K, Babu AM, Sandman K, Reeve JN, Heinemann U J Mol Biol. 2000 Oct 13;303(1):35-47. PMID:11021968<ref>PMID:11021968</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1b6w" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Histone 3D structures\|Histone 3D structures]]		*[[Histone 3D structures\|Histone 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 23:20, 27 December 2023

OCA — Wed, 27 Dec 2023 23:20:11 GMT

←Older revision		Revision as of 23:20, 27 December 2023
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	<StructureSection load='1b6w' size='340' side='right'caption='[[1b6w]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='1b6w' size='340' side='right'caption='[[1b6w]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1b6w]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B6W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1b6w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermus_fervidus Methanothermus fervidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B6W FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non~~-~~Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><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]] 2.05Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=1b6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b6w OCA], [https://pdbe.org/1b6w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b6w RCSB], [https://www.ebi.ac.uk/pdbsum/1b6w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b6w 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=1b6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b6w OCA], [https://pdbe.org/1b6w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b6w RCSB], [https://www.ebi.ac.uk/pdbsum/1b6w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b6w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/HMFB_METFE HMFB_METFE]] Binds and compact DNA (95 to 150 base pairs) to form nucleosome-like structures that contain positive DNA supercoils. Increases the resistance of DNA to thermal denaturation.	+	[https://www.uniprot.org/uniprot/HMFB_METFE HMFB_METFE] Binds and compact DNA (95 to 150 base pairs) to form nucleosome-like structures that contain positive DNA supercoils. Increases the resistance of DNA to thermal denaturation.
	== 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: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Decanniere, K~~]]	+	[[Category: Methanothermus fervidus]]
-	[[Category: ~~Heinemann, U]]~~	+	[[Category: Decanniere K]]
-	~~[[Category: Reeve, J N]]~~	+	[[Category: Heinemann U]]
-	~~[[Category: Sandman,~~ K]]	+	[[Category: Reeve JN]]
-	[[Category: ~~Archaeal histone b~~]]	+	[[Category: Sandman K]]
-	[[Category: ~~Dna binding protein~~]]	+
-	[[Category: ~~Histone]]~~	+
-	~~[[Category: Hmf-2~~]]	+

OCA at 06:57, 24 February 2021

OCA — Wed, 24 Feb 2021 06:57:33 GMT

←Older revision		Revision as of 06:57, 24 February 2021
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	<StructureSection load='1b6w' size='340' side='right'caption='[[1b6w]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='1b6w' size='340' side='right'caption='[[1b6w]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1b6w]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1B6W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1b6w]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B6W FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><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=MSE:SELENOMETHIONINE'>MSE</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=1b6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b6w OCA], [~~http~~://pdbe.org/1b6w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1b6w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1b6w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1b6w 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=1b6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b6w OCA], [https://pdbe.org/1b6w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b6w RCSB], [https://www.ebi.ac.uk/pdbsum/1b6w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b6w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/HMFB_METFE HMFB_METFE]] Binds and compact DNA (95 to 150 base pairs) to form nucleosome-like structures that contain positive DNA supercoils. Increases the resistance of DNA to thermal denaturation.	+	[[https://www.uniprot.org/uniprot/HMFB_METFE HMFB_METFE]] Binds and compact DNA (95 to 150 base pairs) to form nucleosome-like structures that contain positive DNA supercoils. Increases the resistance of DNA to thermal denaturation.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Histone\|Histone]]	+	*[[Histone 3D structures\|Histone 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:55, 21 May 2019

OCA — Tue, 21 May 2019 08:55:59 GMT

←Older revision		Revision as of 08:55, 21 May 2019
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF THE SELENOMETHIONINE VARIANT OF HISTONE HMFB FROM METHANOTHERMUS FERVIDUS==		==CRYSTAL STRUCTURE OF THE SELENOMETHIONINE VARIANT OF HISTONE HMFB FROM METHANOTHERMUS FERVIDUS==
-	<StructureSection load='1b6w' size='340' side='right' caption='[[1b6w]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='1b6w' size='340' side='right'caption='[[1b6w]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1b6w]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B6W FirstGlance]. <br>		<table><tr><td colspan='2'>[[1b6w]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B6W 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/b6/1b6w_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b6/1b6w_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 35:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Decanniere, K]]		[[Category: Decanniere, K]]
	[[Category: Heinemann, U]]		[[Category: Heinemann, U]]

OCA at 06:16, 17 August 2017

OCA — Thu, 17 Aug 2017 06:16:04 GMT

←Older revision		Revision as of 06:16, 17 August 2017
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF THE SELENOMETHIONINE VARIANT OF HISTONE HMFB FROM METHANOTHERMUS FERVIDUS==		==CRYSTAL STRUCTURE OF THE SELENOMETHIONINE VARIANT OF HISTONE HMFB FROM METHANOTHERMUS FERVIDUS==
	<StructureSection load='1b6w' size='340' side='right' caption='[[1b6w]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='1b6w' size='340' side='right' caption='[[1b6w]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1b6w]] is a 1 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Atcc_43054 Atcc 43054]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B6W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1b6w]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B6W FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><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=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HMFB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2180 ATCC 43054])</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=1b6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b6w OCA], [http://pdbe.org/1b6w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1b6w RCSB], [http://www.ebi.ac.uk/pdbsum/1b6w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1b6w ProSAT]</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=1b6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b6w OCA], [http://pdbe.org/1b6w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1b6w RCSB], [http://www.ebi.ac.uk/pdbsum/1b6w PDBsum]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
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=1b6w ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 35:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43054]]
	[[Category: Decanniere, K]]		[[Category: Decanniere, K]]
	[[Category: Heinemann, U]]		[[Category: Heinemann, U]]

OCA at 10:40, 11 September 2015

OCA — Fri, 11 Sep 2015 10:40:36 GMT

←Older revision		Revision as of 10:40, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1b6w' size='340' side='right' caption='[[1b6w]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='1b6w' size='340' side='right' caption='[[1b6w]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1b6w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Methanothermus_fervidus Methanothermus fervidus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B6W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1b6w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43054 Atcc 43054]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B6W FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><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=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HMFB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2180 ~~Methanothermus fervidus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HMFB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2180 ATCC 43054])</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=1b6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b6w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b6w RCSB], [http://www.ebi.ac.uk/pdbsum/1b6w 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=1b6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b6w OCA], [http://pdbe.org/1b6w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1b6w RCSB], [http://www.ebi.ac.uk/pdbsum/1b6w PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1b6w" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Methanothermus fervidus~~]]	+	[[Category: Atcc 43054]]
	[[Category: Decanniere, K]]		[[Category: Decanniere, K]]
	[[Category: Heinemann, U]]		[[Category: Heinemann, U]]

OCA at 15:21, 25 December 2014

OCA — Thu, 25 Dec 2014 15:21:27 GMT

←Older revision		Revision as of 15:21, 25 December 2014
Line 7:		Line 7:
	<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=1b6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b6w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b6w RCSB], [http://www.ebi.ac.uk/pdbsum/1b6w 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=1b6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b6w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b6w RCSB], [http://www.ebi.ac.uk/pdbsum/1b6w PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HMFB_METFE HMFB_METFE]] Binds and compact DNA (95 to 150 base pairs) to form nucleosome-like structures that contain positive DNA supercoils. Increases the resistance of DNA to thermal denaturation.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:50, 22 December 2014

OCA — Mon, 22 Dec 2014 08:50:24 GMT

←Older revision		Revision as of 08:50, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1b6w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermus_fervidus Methanothermus fervidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B6W FirstGlance]. <br>		<table><tr><td colspan='2'>[[1b6w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermus_fervidus Methanothermus fervidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B6W FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><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=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HMFB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2180 Methanothermus fervidus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HMFB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2180 Methanothermus fervidus])</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=1b6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b6w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b6w RCSB], [http://www.ebi.ac.uk/pdbsum/1b6w 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=1b6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b6w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b6w RCSB], [http://www.ebi.ac.uk/pdbsum/1b6w PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Methanothermus fervidus]]		[[Category: Methanothermus fervidus]]
-	[[Category: Decanniere, K.]]	+	[[Category: Decanniere, K]]
-	[[Category: Heinemann, U.]]	+	[[Category: Heinemann, U]]
-	[[Category: Reeve, J N.]]	+	[[Category: Reeve, J N]]
-	[[Category: Sandman, K.]]	+	[[Category: Sandman, K]]
	[[Category: Archaeal histone b]]		[[Category: Archaeal histone b]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: Histone]]		[[Category: Histone]]
	[[Category: Hmf-2]]		[[Category: Hmf-2]]

OCA at 03:23, 7 August 2014

OCA — Thu, 07 Aug 2014 03:23:11 GMT

←Older revision		Revision as of 03:23, 7 August 2014
Line 1:		Line 1:
-	[[~~Image:~~1b6w.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF THE SELENOMETHIONINE VARIANT OF HISTONE HMFB FROM METHANOTHERMUS FERVIDUS==
		+	<StructureSection load='1b6w' size='340' side='right' caption='[[1b6w]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1b6w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermus_fervidus Methanothermus fervidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B6W FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HMFB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2180 Methanothermus fervidus])</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=1b6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b6w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b6w RCSB], [http://www.ebi.ac.uk/pdbsum/1b6w 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/b6/1b6w_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 ==
		+	The hyperthermophilic archaeon Methanothermus fervidus contains two small basic proteins, HMfA (68 amino acid residues) and HMfB (69 residues) that share a common ancestry with the eukaryal nucleosome core histones H2A, H2B, H3, and H4. HMfA and HMfB have sequences that differ at 11 locations, they have different structural stabilities, and the complexes that they form with DNA have different electrophoretic mobilities. Here, crystal structures are documented for recombinant (r) HMfA at a resolution of 1.55 A refined to a crystallographic R-value of 19.8 % (tetragonal form) and at 1.48 A refined to a R-value of 18.8 % (orthorhombic form), and for rHMfB at 1.9 A refined to a R-value of 18.0 %. The rHMfA and rHMfB monomers have structures that are just histone folds in which a long central alpha-helix (alpha2; 29 residues) is separated from shorter N-terminal (alpha1; 11 residues) and C-terminal (alpha3; 10 residues) alpha-helices by two loops (L1 and L2; both 6 residues). Within L1 and L2, three adjacent residues are in extended (beta) conformation. rHMfA and rHMfB assemble into homodimers, with the alpha2 helices anti-parallel aligned and crossing at an angle of close to 35 degrees, and with hydrogen bonds formed between the extended, parallel regions of L1 and L2 resulting in short beta-ladders. Dimerization creates a novel N-terminal structure that contains four proline residues, two from each monomer. As prolines are present at these positions in all archaeal histone sequences, this proline-tetrad structure is likely to be a common feature of all archaeal histone dimers. Almost all residues that participate in monomer-monomer interactions are conserved in HMfA and HMfB, consistent with the ability of these monomers to form both homodimers and (HMfA+HMfB) heterodimers. Differences in side-chain interactions that result from non-conservative residue differences in HMfA and HMfB are identified, and the structure of a (rHMfA)(2)-DNA complex is presented based on the structures documented here and modeled by homology to histone-DNA interactions in the eukaryal nucleosome.

-	~~{{STRUCTURE_1b6w\| PDB=1b6w \| SCENE= }}~~	+	Crystal structures of recombinant histones HMfA and HMfB from the hyperthermophilic archaeon Methanothermus fervidus.,Decanniere K, Babu AM, Sandman K, Reeve JN, Heinemann U J Mol Biol. 2000 Oct 13;303(1):35-47. PMID:11021968<ref>PMID:11021968</ref>

-	~~===CRYSTAL STRUCTURE OF THE SELENOMETHIONINE VARIANT OF HISTONE HMFB FROM METHANOTHERMUS FERVIDUS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11021968}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1b6w]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Methanothermus_fervidus Methanothermus fervidus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1B6W OCA].~~	+

	==See Also==		==See Also==
	*[[Histone\|Histone]]		*[[Histone\|Histone]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:011021968<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Methanothermus fervidus]]		[[Category: Methanothermus fervidus]]
	[[Category: Decanniere, K.]]		[[Category: Decanniere, K.]]

OCA at 18:15, 20 October 2012

OCA — Sat, 20 Oct 2012 18:15:53 GMT

←Older revision		Revision as of 18:15, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1b6w]] is a 1 chain structure ~~of [[Histone]]~~ with sequence from [http://en.wikipedia.org/wiki/Methanothermus_fervidus Methanothermus fervidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6W OCA].	+	[[1b6w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermus_fervidus Methanothermus fervidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6W OCA].

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