Nucleosomes: Difference between revisions

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This page offers some large scenes of a nucleosome ([[1aoi]]) suitable for projection in biochemistry classes. For a general introduction, see Wikipedia: [http://en.wikipedia.org/wiki/Nucleosomes Nucleosome]. For a list of nucleosome PDB entries, see [[:Category:Nucleosome | Category: Nucleosome]] .
For a general introduction beyond what is provided below, please see Wikipedia: [http://en.wikipedia.org/wiki/Nucleosomes Nucleosome]. For a list of nucleosome structures, see [[:Category:Nucleosome | Category: Nucleosome]].


==Scenes for Projection in Biochemistry Classes==
==Scenes for Projection in Biochemistry Classes==
<applet load="1aoi" size="600" color="white" frame="true" align="right" spinBox="true"
 
caption="1aoi, resolution 2.80&Aring;" />
This section offers some large scenes of a nucleosome ([[1aoi]]), as determined in [http://www.mol.biol.ethz.ch/groups/richmond  Tim Richmond's lab], suitable for projection in biochemistry classes.
 
<applet load="1aoi" size="450" color="white" frame="true" align="right" caption="[[1aoi]], resolution 2.80&Aring;" script="Nucleosomes/Rockets/1" />


<big>
<big>
1. '''<scene name='Nucleosomes/Composition/1'>Composition</scene>: <font color='#808080'>DNA</font>, <font color='#7e6c54'>Protein</font>.'''
1. '''<scene name='Nucleosomes/Composition/2'>Composition</scene>: <font color='#808080'>DNA</font>, <font color='#7e6c54'>Protein</font>.'''


2. '''<scene name='Nucleosomes/Dna/2'>DNA</scene>'''
2. '''<scene name='Nucleosomes/Dna/3'>DNA</scene>'''
<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>display displayed,*:i,*:j</scriptWhenChecked>
    <scriptWhenUnchecked>hide hidden,*:i,*:j</scriptWhenUnchecked>
    <checked>true</checked>
    <text></text>
  </jmolCheckbox>
</jmol>


<big>Histone color key: '''<font color='red'>H2a</font> <font color='orange'>H2b</font> <font color='green'>H3</font> <font color='blue'>H4</font>'''</big>
3. '''<scene name='Nucleosomes/Histones/6'>Histones</scene>'''
 
''These checkboxes do not work''
<br>
<br>
Hide:
&nbsp;&nbsp;
<jmol>
<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>"restrict not (:c,:g)"</scriptWhenChecked>
     <scriptWhenChecked>display displayed,*:c,*:g</scriptWhenChecked>
     <scriptWhenUnchecked></scriptWhenUnchecked>
     <scriptWhenUnchecked>hide hidden,*:c,*:g</scriptWhenUnchecked>
     <text>H2a</text>
    <checked>true</checked>
     <text></text>
   </jmolCheckbox>
   </jmolCheckbox>
</jmol>
</jmol><big>'''<font color='red'>H2a</font>'''</big>
&nbsp;
<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>display displayed,*:d,*:h</scriptWhenChecked>
    <scriptWhenUnchecked>hide hidden,*:d,*:h</scriptWhenUnchecked>
    <checked>true</checked>
    <text></text>
  </jmolCheckbox>
</jmol><big>'''<font color='orange'>H2b</font>'''</big>
&nbsp;
&nbsp;
<jmol>
<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>'restrict not (:a,:e)'</scriptWhenChecked>
     <scriptWhenChecked>display displayed,*:a,*:e</scriptWhenChecked>
     <scriptWhenUnchecked></scriptWhenUnchecked>
     <scriptWhenUnchecked>hide hidden,*:a,*:e</scriptWhenUnchecked>
     <text>H3</text>
    <checked>true</checked>
     <text></text>
   </jmolCheckbox>
   </jmolCheckbox>
</jmol>
</jmol><big>'''<font color='green'>H3</font>'''</big>
&nbsp;
&nbsp;
<jmol>
<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>restrict not (:b,:f)</scriptWhenChecked>
     <scriptWhenChecked>display displayed,*:b,*:f</scriptWhenChecked>
     <text>H4</text>
    <scriptWhenUnchecked>hide hidden,*:b,*:f</scriptWhenUnchecked>
    <checked>true</checked>
     <text></text>
   </jmolCheckbox>
   </jmolCheckbox>
</jmol>
</jmol><big>'''<font color='blue'>H4</font>'''</big>
 
 
4. '''<scene name='Nucleosomes/Rockets/4'>Secondary Structure</scene>'''


3. '''<scene name='Nucleosomes/Histones/2'>Histones</scene>'''
<ul>
<li><scene name='Nucleosomes/Rockets/10'>H2a and H2b only</scene></li>
<li><scene name='Nucleosomes/Rockets/11'>H3 and H4 only</scene></li>
</ul>


4. '''<scene name='Nucleosomes/Rockets/1'>Secondary Structure</scene>'''
</big>
</big>
<scene name='1aoi/Introduction/2'>The nucleosome core particle</scene> contains two copies of each histone <font color=tan>'''protein'''</font> (<font color=tan>'''H2A, H2B, H3, H4'''</font>) and 146 basepairs (bp) of superhelical <font color=purple>'''DNA'''</font> wrapped around this histone octamer. It represents the first order of DNA packaging in the nucleus and as such is the principal structure that determines DNA accessibility (this scene was created by David Marcey, Eran Hodis, Jaime Prilusky).<br />
Examples of [[Archaeal_Histones]]
<br clear='right'>
==3D structures of histone==
[[Histone]]
==Additional Resources==
For Additional Information, See: [[Nucleic Acids]]
== Files for 3D printer ==
<i class="fas fa-cubes"></i> Nucleosome by [[User:Marius Mihasan|Marius Mihasan]] [https://3dprint.nih.gov/discover/3DPX-015090  <i class="fas fa-download"></i>]


[[Category:Nucleosome]]
[[Category:Nucleosome]]
[[Category:3D printer files]]

Latest revision as of 17:27, 4 January 2022

For a general introduction beyond what is provided below, please see Wikipedia: Nucleosome. For a list of nucleosome structures, see Category: Nucleosome.

Scenes for Projection in Biochemistry ClassesScenes for Projection in Biochemistry Classes

This section offers some large scenes of a nucleosome (1aoi), as determined in Tim Richmond's lab, suitable for projection in biochemistry classes.

1aoi, resolution 2.80Å

Drag the structure with the mouse to rotate

1. : DNA, Protein.

2.

3.
   H2a   H2b   H3   H4


4.

contains two copies of each histone protein (H2A, H2B, H3, H4) and 146 basepairs (bp) of superhelical DNA wrapped around this histone octamer. It represents the first order of DNA packaging in the nucleus and as such is the principal structure that determines DNA accessibility (this scene was created by David Marcey, Eran Hodis, Jaime Prilusky).
Examples of Archaeal_Histones

3D structures of histone3D structures of histone

Histone

Additional ResourcesAdditional Resources

For Additional Information, See: Nucleic Acids

Files for 3D printerFiles for 3D printer

Nucleosome by Marius Mihasan

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Eran Hodis, Joel L. Sussman, Harry Greenblatt, Jaime Prilusky, Angel Herraez, David Canner, Michal Harel, Karl Oberholser, Alexander Berchansky
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