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New page: left|200px<br /><applet load="2aro" size="450" color="white" frame="true" align="right" spinBox="true" caption="2aro, resolution 2.10Å" /> '''Crystal Structure Of...
 
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[[Image:2aro.gif|left|200px]]<br /><applet load="2aro" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2aro, resolution 2.10&Aring;" />
'''Crystal Structure Of The Native Histone Octamer To 2.1 Angstrom Resolution, Crystalised In The Presence Of S-Nitrosoglutathione'''<br />


==Overview==
==Crystal Structure Of The Native Histone Octamer To 2.1 Angstrom Resolution, Crystalised In The Presence Of S-Nitrosoglutathione==
A H3 dimer band is produced when purified native histone octamers are run, on an SDS-PAGE gel in a beta-mercaptoethanol-free environment. To, investigate this, native histone octamer crystals, derived from chicken, erythrocytes, and of structure (H2A-H2B)-(H4-H3)-(H3'-H4')-(H2B'-H2A'), were grown in 2 M KCl, 1.35 M potassium phosphates and 250-350 microM of, the oxidising agent S-nitrosoglutathione, pH 6.9. X-ray diffraction data, were acquired to 2.10 A resolution, yielding a structure with an Rwork, value of 18.6% and an Rfree of 22.5%. The space group is P6(5), the, asymmetric unit of which contains one complete octamer. Compared to the, 1.90 A resolution, unoxidised native histone octamer structure, the, crystals show a reduction of 2.5% in the c-axis of the unit cell, and, free-energy calculations reveal that the H3-H3' dimer interface in the, latter has become thermodynamically stable, in contrast to the former., Although the inter-sulphur distance of the two H3 cysteines in the, oxidised native histone octamer has reduced to 6 A from the 7 A of the, unoxidised form, analysis of the hydrogen bonds that constitute the, (H4-H3)-(H3'-H4') tetramer indicates that the formation of a disulphide, bond in the H3-H3' dimer interface is incompatible with stable tetramer, formation. The biochemical and biophysical evidence, taken as a whole, is, indicative of crystals that have a stable H3-H3' dimer interface, possibly, extending to the interface within an isolated H3-H3' dimer, observed in, SDS-PAGE gels.
<StructureSection load='2aro' size='340' side='right'caption='[[2aro]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2aro]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ARO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ARO FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=2aro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aro OCA], [https://pdbe.org/2aro PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2aro RCSB], [https://www.ebi.ac.uk/pdbsum/2aro PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2aro ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/H2A4_CHICK H2A4_CHICK] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.
== 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/ar/2aro_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/main_output.php?pdb_ID=2aro ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A H3 dimer band is produced when purified native histone octamers are run on an SDS-PAGE gel in a beta-mercaptoethanol-free environment. To investigate this, native histone octamer crystals, derived from chicken erythrocytes, and of structure (H2A-H2B)-(H4-H3)-(H3'-H4')-(H2B'-H2A'), were grown in 2 M KCl, 1.35 M potassium phosphates and 250-350 microM of the oxidising agent S-nitrosoglutathione, pH 6.9. X-ray diffraction data were acquired to 2.10 A resolution, yielding a structure with an Rwork value of 18.6% and an Rfree of 22.5%. The space group is P6(5), the asymmetric unit of which contains one complete octamer. Compared to the 1.90 A resolution, unoxidised native histone octamer structure, the crystals show a reduction of 2.5% in the c-axis of the unit cell, and free-energy calculations reveal that the H3-H3' dimer interface in the latter has become thermodynamically stable, in contrast to the former. Although the inter-sulphur distance of the two H3 cysteines in the oxidised native histone octamer has reduced to 6 A from the 7 A of the unoxidised form, analysis of the hydrogen bonds that constitute the (H4-H3)-(H3'-H4') tetramer indicates that the formation of a disulphide bond in the H3-H3' dimer interface is incompatible with stable tetramer formation. The biochemical and biophysical evidence, taken as a whole, is indicative of crystals that have a stable H3-H3' dimer interface, possibly extending to the interface within an isolated H3-H3' dimer, observed in SDS-PAGE gels.


==About this Structure==
The oxidised histone octamer does not form a H3 disulphide bond.,Wood CM, Sodngam S, Nicholson JM, Lambert SJ, Reynolds CD, Baldwin JP Biochim Biophys Acta. 2006 Aug;1764(8):1356-62. Epub 2006 Jul 21. PMID:16920041<ref>PMID:16920041</ref>
2ARO is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] with PO4 and CL as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2ARO OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
The oxidised histone octamer does not form a H3 disulphide bond., Wood CM, Sodngam S, Nicholson JM, Lambert SJ, Reynolds CD, Baldwin JP, Biochim Biophys Acta. 2006 Aug;1764(8):1356-62. Epub 2006 Jul 21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16920041 16920041]
</div>
<div class="pdbe-citations 2aro" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Histone 3D structures|Histone 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Gallus gallus]]
[[Category: Gallus gallus]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Baldwin, J.P.]]
[[Category: Baldwin JP]]
[[Category: Lambert, S.J.]]
[[Category: Lambert SJ]]
[[Category: Nicholson, J.M.]]
[[Category: Nicholson JM]]
[[Category: Reynolds, C.D.]]
[[Category: Reynolds CD]]
[[Category: Sodngam, S.]]
[[Category: Sodngam S]]
[[Category: Wood, C.M.]]
[[Category: Wood CM]]
[[Category: CL]]
[[Category: PO4]]
[[Category: allostery]]
[[Category: circular dichroism]]
[[Category: octamer]]
[[Category: oxidation]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 08:19:18 2007''

Latest revision as of 10:28, 23 August 2023

Crystal Structure Of The Native Histone Octamer To 2.1 Angstrom Resolution, Crystalised In The Presence Of S-NitrosoglutathioneCrystal Structure Of The Native Histone Octamer To 2.1 Angstrom Resolution, Crystalised In The Presence Of S-Nitrosoglutathione

Structural highlights

2aro is a 8 chain structure with sequence from Gallus gallus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

H2A4_CHICK Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

A H3 dimer band is produced when purified native histone octamers are run on an SDS-PAGE gel in a beta-mercaptoethanol-free environment. To investigate this, native histone octamer crystals, derived from chicken erythrocytes, and of structure (H2A-H2B)-(H4-H3)-(H3'-H4')-(H2B'-H2A'), were grown in 2 M KCl, 1.35 M potassium phosphates and 250-350 microM of the oxidising agent S-nitrosoglutathione, pH 6.9. X-ray diffraction data were acquired to 2.10 A resolution, yielding a structure with an Rwork value of 18.6% and an Rfree of 22.5%. The space group is P6(5), the asymmetric unit of which contains one complete octamer. Compared to the 1.90 A resolution, unoxidised native histone octamer structure, the crystals show a reduction of 2.5% in the c-axis of the unit cell, and free-energy calculations reveal that the H3-H3' dimer interface in the latter has become thermodynamically stable, in contrast to the former. Although the inter-sulphur distance of the two H3 cysteines in the oxidised native histone octamer has reduced to 6 A from the 7 A of the unoxidised form, analysis of the hydrogen bonds that constitute the (H4-H3)-(H3'-H4') tetramer indicates that the formation of a disulphide bond in the H3-H3' dimer interface is incompatible with stable tetramer formation. The biochemical and biophysical evidence, taken as a whole, is indicative of crystals that have a stable H3-H3' dimer interface, possibly extending to the interface within an isolated H3-H3' dimer, observed in SDS-PAGE gels.

The oxidised histone octamer does not form a H3 disulphide bond.,Wood CM, Sodngam S, Nicholson JM, Lambert SJ, Reynolds CD, Baldwin JP Biochim Biophys Acta. 2006 Aug;1764(8):1356-62. Epub 2006 Jul 21. PMID:16920041[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Wood CM, Sodngam S, Nicholson JM, Lambert SJ, Reynolds CD, Baldwin JP. The oxidised histone octamer does not form a H3 disulphide bond. Biochim Biophys Acta. 2006 Aug;1764(8):1356-62. Epub 2006 Jul 21. PMID:16920041 doi:10.1016/j.bbapap.2006.06.014

2aro, resolution 2.10Å

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