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[[Image:2cv5.gif|left|200px]]<br /><applet load="2cv5" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2cv5, resolution 2.5&Aring;" />
'''Crystal structure of human nucleosome core particle'''<br />


==Overview==
==Crystal structure of human nucleosome core particle==
Gene expression in eukaryotes depends upon positioning, mobility and packaging of nucleosomes; thus, we need the detailed information of the human nucleosome core particle (NCP) structure, which could clarify chromatin properties. Here, we report the 2.5 A crystal structure of a human NCP. The overall structure is similar to those of other NCPs reported previously. However, the DNA path of human NCP is remarkably different from that taken within other NCPs with an identical DNA sequence. A comparison of the structural parameters between human and Xenopus laevis DNA reveals that the DNA path of human NCP consecutively shifts by 1 bp in the regions of superhelix axis location -5.0 to -2.0 and 5.0 to 7.0. This alteration of the human DNA path is caused predominantly by tight DNA-DNA contacts within the crystal. It is also likely that the conformational change in the human H2B tail induces the local alteration of the DNA path. In human NCP, the region with the altered DNA path lacks Mn2+ ions and the B-factors of the DNA phosphate groups are substantially high. Therefore, in contrast to the histone octamer, the nucleosomal DNA is sufficiently flexible and mobile and can undergo drastic conformational changes, depending upon the environment.
<StructureSection load='2cv5' size='340' side='right'caption='[[2cv5]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2cv5]] is a 10 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=2CV5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CV5 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]] 2.5&#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=MN:MANGANESE+(II)+ION'>MN</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=2cv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cv5 OCA], [https://pdbe.org/2cv5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cv5 RCSB], [https://www.ebi.ac.uk/pdbsum/2cv5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cv5 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/H31_HUMAN H31_HUMAN]
== 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/cv/2cv5_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=2cv5 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2CV5 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=MN:'>MN</scene> and <scene name='pdbligand=CL:'>CL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CV5 OCA].
*[[Histone 3D structures|Histone 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle., Tsunaka Y, Kajimura N, Tate S, Morikawa K, Nucleic Acids Res. 2005 Jun 10;33(10):3424-34. Print 2005. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15951514 15951514]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Kajimura, N.]]
[[Category: Kajimura N]]
[[Category: Morikawa, K.]]
[[Category: Morikawa K]]
[[Category: Tate, S.]]
[[Category: Tate S]]
[[Category: Tsunaka, Y.]]
[[Category: Tsunaka Y]]
[[Category: CL]]
[[Category: MN]]
[[Category: human nucleosome structure]]
[[Category: metal binding site]]
[[Category: supercoiled dna path]]
[[Category: x-ray crystallography]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:52:44 2008''

Latest revision as of 16:43, 13 March 2024

Crystal structure of human nucleosome core particleCrystal structure of human nucleosome core particle

Structural highlights

2cv5 is a 10 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

H31_HUMAN

Evolutionary Conservation

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

See Also

2cv5, resolution 2.50Å

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