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{{STRUCTURE_2hue|  PDB=2hue | SIZE=400| SCENE= |right|CAPTION=Yeast H3 (green), H4 (pink) and anti-silencing protein (grey) complex with sulfate, glycerol and Zn+2 ion (grey), [[2hue]] }}
<StructureSection load='2hue' size='340' side='right' caption='Yeast H3 (green), H4 (pink) and anti-silencing protein (grey) complex with sulfate, glycerol and Zn+2 ion (grey), [[2hue]]' scene=''>
==Histone core protein structure==
'''Histones''' are highly <scene name='Taylor_histone_sandbox/Conservation/1'>conserved proteins</scene> (more purple = more conserved) with <scene name='Taylor_histone_sandbox/Charge_distribution/1'>positive charge</scene> (blue is positive charge, red is negative charge).  Because of this positive charge, they interact electrostatically with the negatively charged phosphate groups in DNA. 
There are five major classes of histones: H1/H5, H2A, H2B, H3, and H4.<ref>PMID: 16472024</ref><ref name="Voet, Voet, and Pratt">{{Cite book|surname1= Voet|given1= Donald |surname2= Voet|given2= Judith|surname3= Pratt|given3= Leon A.|  year=1988|title=Basic Genetics|publication-place=Boston|publisher=Jones and Bartlett Publishers|isbn=0-86720-090-1}}</ref> Histones <scene name='46/468228/2a/3'>H2A</scene>, <scene name='46/468228/2b/4'>H2B</scene>, <scene name='46/468228/3/3'>H3</scene>, and <scene name='46/468228/H4/1'>H4</scene> are known as the core histones, while histones H1 and H5 are known as the linker histones.


'''Histones''' (H) are the major protein components of chromatin which help to pack the DNA in the nucleosomes. H2A, H2B, H3 and H4 are core histones while H1 and H5 are linker histones.  See details in [[nucleosomes]]. For the hyperthermophilic histones see [[Archaeal Histones]].  For nucleosome structure see [[User:Eric Martz/Nucleosomes]] and [[Nucleosomes]].
The 4 'core' histones (H2A, H2B, H3 and H4) are relatively similar in structure and are highly conserved through evolution, all featuring a <scene name='Taylor_histone_sandbox/N_c_rainbow/1'>'helix turn helix turn helix' </scene> motif (which allows the easy dimerization).  They also share the feature of long 'tails' on one end of the amino acid structure, which are often covalently modified to regulate gene expression.   


== 3D Structures of histone == 


Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#tree:id=OrganizedByTopic|openlevels=0|


*Histone
== Histone interactions with DNA ==


**[[1yqa]] – yH1 (mutant) – yeast – NMR<BR />
Histones are the chief protein components of <scene name='46/468228/Nucleosome/1'>chromatin</scene>, acting as spools around which DNA winds, and play a role in gene regulation. Without histones, the unwound DNA in chromosomes would be very long;  each human cell has about 1.8 meters of DNA, but wound on the histones it has about 90 micrometers (0.09&nbsp;mm) of chromatin, which, when duplicated and condensed during mitosis, result in about 120 micrometers of chromosomes.<ref name="pmid11893489">PMID: 11893489</ref> DNA is wrapped around nucleosomes with approximately 50 base pairs of DNA between subsequent nucleosomes (also referred to as linker DNA). The assembled histones and DNA is called chromatin. During mitosis and meiosis, the condensed chromosomes are assembled through interactions between nucleosomes and other regulatory proteins.
**[[1uss]], [[1ust]], [[1uhm]] – yH1 globular domain - NMR<BR />
**[[1ghc]] – cH1 – chicken - NMR<br />
**[[2xd7]], [[1zr3]], [[1zr5]], [[2fxk]] – hH2A macro domain – human<BR />
**[[4cay]] – hH2A +H2B<br />
**[[1yd9]] – H2A macro domain – rat<BR />
**[[1ku5]] – HPHA – ''Pyrococcus horikoshii''<BR />
**[[1b67]], [[1b6w]], [[1a7w]], [[1hta]] – MfHMFA – ''Methanococcus fervidus''<BR />
**[[1bfm]] – MfHB - NMR<BR />
**[[1f1e]] – H – ''Methanopyrus kandleri''<BR />
**[[1hst]] – cH5 <BR />
**[[3iid]], [[3iif]] – H2A macro domain + ADP-ribose<BR />
**[[2g9a]], [[2g99]], [[2h13]] – H3 + WD-repeat protein<br />
**[[1pfb]] – H3 + polycomb protein – ''Strongylocentrus purpuratus''


*Nucleosome core
The '''nucleosome''' core is formed of two <scene name='46/468228/H2a_h2b_dimer/1'>H2A-H2B dimers</scene> and a <scene name='46/468228/H4_h3_tetramer/1'>H3-H4 tetramer</scene>, forming two nearly <scene name='46/468228/Nucleosome_dimer/1'>symmetrical halves</scene> by tertiary structure.<ref name=pmid9305837/>  147 base pairs of <scene name='46/468228/Dna_wrap_around_histone/1'>DNA wrap</scene> around this core particle 1.65 times in a left-handed super-helical turn.<ref name=pmid9305837>PMID: 9305837</ref>  The linker histone H1 binds the nucleosome and the entry and exit sites of the DNA, thus locking the DNA into place<ref name="isbn0-915274-84-1">{{cite book |author=Farkas, Daniel |title=DNA simplified: the hitchhiker's guide to DNA |publisher=AACC Press |location=Washington, D.C |year=1996 |isbn=0-915274-84-1 }}</ref> and allowing the formation of higher order structure. 


**[[3r45]] - hH4 + H3-like centromeric protein + Holliday junction recognition protein<BR />
The '''chromatosome''' contains histone H1 binding to nucleosome.  It contains 166 DNA base pairs.  
**[[3nqj]], [[3nqu]] - hH4 + H3-like centromeric protein<BR />
**[[4h9n]], [[4h9o]], [[4h9p]], [[4h9q]], [[4h9r]], [[4h9s]], [[4hga]] - XlH3.3 (mutant) + H4 + death domain-associated protein 6<br />
**[[3qzs]], [[3qzt]] – XlH4 + nucleosome-remodeling factor subunit BPTF – ''Xenopus laevis''<BR />
**[[2io5]] - XlH3.1 + H4 + anti-silencing protein<BR />
**[[4eo5]] - XlH3.2 (mutant) + H4 (mutant) + histone chaperone ASF1<br />
**[[4ld9]] - XlH3.2 + H4 + H2A + H2B + widom sequence reverse + SIR3<br />
**[[2yfv]], [[2yfw]] - H4 + H3-like centromeric protein + SCM3 – ''Kluyveromyces lactis''<BR />
**[[2l5a]] - yH4/H3-like centromeric protein/SCM3<BR />
**[[2jss]] - yH2A/H2B + CHZ1 – NMR<BR />
**[[2hue]] - yH3 + H4 + anti-silencing protein<BR />
**[[2xql]], [[3c9k]] - cH3.2 + H4 + H2A + H2B – EM


*Nucleosome core + DNA
 
In all, histones make five types of interactions with DNA:
*<scene name='Taylor_histone_sandbox/Rockets/1'>Helix-dipoles</scene> from alpha-helices in H2B, H3, and H4 cause a net positive charge to accumulate at the point of interaction with negatively charged phosphate groups on DNA
*Hydrogen bonds between the DNA backbone and the peptide bond in the backbone of histone proteins
*Interactions between the histone and deoxyribose sugars on DNA
*<scene name='46/468228/Tails_charge/1'>salt bridges and hydrogen bonds </scene> between side chains of basic amino acids (especially lysine and arginine) and phosphate oxygens on DNA
*Non-specific minor groove insertions of the H3 and H2B <scene name='46/468228/Tails/2'>N terminal tails</scene> into two minor grooves each on the DNA molecule


**[[3an2]] – hH4 + H2A + H2B + H3-like centromeric protein + DNA<BR />
**[[3av1]], [[2av2]], [[3av2]], [[3waa]], [[3wa9]], [[3w99]], [[3w98]], [[3w97]], [[3w96]] – hH3.2 + H4 + H2A + H2B + DNA<BR />
**[[3a6n]], [[3afa]], [[2cv5]] - hH3.1 + H4 + H2A + H2B + DNA<BR />
**[[3ayw]], [[3aze]], [[3azf]], [[3azg]], [[3azh]] - hH3.1 (mutant) + H4 + H2A + H2B + DNA<br />
**[[3azi]], [[3azj]], [[3azk]], [[3azl]], [[3azm]], [[3azn]] - hH3.1 + H4 (mutant) + H2A + H2B + DNA<br />
**[[3mnn]], [[3o62]], [[3lz0]], [[3lz1]], [[3lel]], [[3kuy]], [[3c1b]], [[3c1c]], [[2nzd]], [[2fj7]], [[1zbb]], [[1s32]], [[1p34]], [[1p3a]], [[1p3b]], [[1p3f]], [[1p3g]], [[1p3i]], [[1p3k]], [[1p3l]], [[1p3m]], [[1p3o]], [[1p3p]], [[1m18]], [[1m19]], [[1m1a]], [[1kx3]], [[1kx4]], [[1kx5]], [[1aoi]],  [[3reh]], [[3rei]], [[3rej]], [[3rek]], [[3rel]], [[3ut9]], [[3uta]], [[3utb]] - XlH3.2 + H4 + H2A + H2B + DNA<BR />
**[[2f8n]] - XlH3.1 + H4 + H2A + H2B + H3 + H2A macro domain + DNA<BR />
**[[1zla]] – XlH3 + H4 + H2A + H2B + H3 + antigen + DNA<BR />
**[[3mgp]], [[3mgq]], [[3mgr]], [[3mgs]], [[3lja]], [[3b6f]], [[3b6g]], [[4j8u]], [[4j8v]], [[4j8w]], [[4j8x]] - XlH3.2 + H4 + H2A + H2B + metal ion + DNA<BR />
**[[3kxb]] - XlH3.2 (mutant) + H4 + H2A + H2B (mutant) + DNA<BR />
**[[3kwq]] - XlH3.2 (mutant) + H4 + H2A + H2B + DNA<BR />
**[[3mvd]] - XlH3.2 + H4 + H2A + H2B + regulator of chromosome condensation + DNA<BR />
**[[3tu4]] - XlH3.2 + H4 + H2A + H2B + regulatory protein SIR3 + DNA<br />
**[[1id3]] - yH3 + H4 + H2A + H2B + DNA<BR />
**[[4jjn]], [[4kud]] - yH3 + H4 + H2A.2 + H2B.2 + SIR3 + DNA<br />
**[[2aro]], [[1tzy]], [[1hq3]], [[2hio]], [[1hio]] - cH3 + H4 + H2A + H2B<br />
**[[1eqz]] - cH3 + H4 + H2A + H2B + DNA<BR />
**[[2pyo]], [[2nqb]], [[3nqb]] - DmH3 + H4 + H2A + H2B + DNA – ''Drosophila melanogaster''<BR />
**[[4inm]] - DmH3 + H4 + H2A + H2B + centromeric protein C + DNA<br />
**[[1u35]] - mH3.1 + H2A + H2B + His2A macro domain + DNA – mouse<BR />
**[[1f66]] - XlH3 + mH4 + hH2A + XlH2B + DNA<BR />
}}


In general, genes that are active have less bound histone, while inactive genes are highly associated with histones during interphase.  It also appears that the structure of histones has been evolutionarily conserved, as any deleterious mutations would be severely maladaptive.


=== Chromatin regulation ===


Histones are subject to post translational modification by enzymes primarily on their N-terminal tails, but also in their globular domains.  Such modifications include methylation, acetylation, phosphorylation, SUMOylation, ubiquitination, and ADP-ribosylation. This affects gene expression. The core of the histones H2A, H2B, and H3 can also be modified. Combinations of modifications are thought to constitute a code, the so-called "histone code".<ref name=pmid10638745>PMID: 10638745</ref><ref name=pmid11498575>PMID: 11498575</ref> Histone modifications act in diverse biological processes such as gene regulation, DNA repair, chromosome condensation (in mitosis, spermatogenesis, and meiosis).<ref>PMID: 21927517</ref>


The common nomenclature of histone modifications is:
*The name of the histone (e.g., H3)
*The single-letter amino acid abbreviation (e.g., K for Lysine) and the amino acid position in the protein
*The type of modification (Me: methyl, P: phosphate, Ac: acetylation, Ub: [[ubiquitin]])


So H3K4me1 denotes the monomethylation of the 4th residue (a lysine) from the start (i.e., the N-terminal) of the H3 protein.


</StructureSection>


* For nucleosome structure see<br />
* [[User:Eric Martz/Nucleosomes]]<br />
* [[Nucleosome structure]]<br />
* [[Nucleosomes]]<br />
* [[Nucleosome structure (Spanish)]]<br />


== 3D Structures of histone ==
[[Histone 3D structures]]




== References ==
<references/>


[[Category:Topic Page]]
[[Category:Topic Page]]

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

Michal Harel, Alexander Berchansky, Ann Taylor, Karsten Theis
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