SMART: H3 domain annotation

H3 Histone H3

SMART accession number:	SM00428
Description:
Interpro abstract (IPR000164):	Histone H3 is one of the four histones, along with H2A, H2B and H4, which form the eukaryotic nucleosome octomer core [(PUBMED:8121801)]; the nucleosome octamer winds ~146 DNA base-pairs. It is a highly conserved protein of 135 amino acid residues [(PUBMED:8121801), (PUBMED:2041803)]. Several proteins have been found to contain a C-terminal H3-like domain, including the mammalian centromeric protein CENP-A (which may act as a core histone necessary for the assembly of centromeres) [(PUBMED:7962047)]; yeast chromatin- associated protein CSE4 [(PUBMED:7698647)]; and Caenorhabditis elegans chromosome III proteins YL82_CAEEL and YMH3_CAEEL, whose function is unknown.
GO process:	nucleosome assembly (GO:0006334)
GO component:	nucleosome (GO:0000786)
GO function:	DNA binding (GO:0003677)
Family alignment:	View or

There are 1826 H3 domains in 1825 proteins in SMART's nrdb database.

Click on the following links for more information.

Evolution (species in which this domain is found)
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This tree shows only several representative species. The complete taxonomic breakdown of all proteins with H3 domain is also avaliable.

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Go to specific node: Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Takifugu rubripes
Literature (relevant references for this domain)
Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.
- Luger K, Richmond TJ
- DNA binding within the nucleosome core.
- Curr Opin Struct Biol. 1998; 8: 33-40
- Display abstract
- The high resolution structure of the nucleosome core particle of chromatin reveals the form of DNA that is predominant in living cells and offers a wealth of information on DNA binding and bending by the histone octamer. Recent studies imply that chromatin is highly dynamic. This propensity for unfolding and refolding stems from the structural design of the nucleosome core. The histone-fold motif, central to nucleosome structure, is also found in other proteins involved in transcriptional regulation.
- Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ
- Crystal structure of the nucleosome core particle at 2.8 A resolution.
- Nature. 1997; 389: 251-60
- Display abstract
- The X-ray crystal structure of the nucleosome core particle of chromatin shows in atomic detail how the histone protein octamer is assembled and how 146 base pairs of DNA are organized into a superhelix around it. Both histone/histone and histone/DNA interactions depend on the histone fold domains and additional, well ordered structure elements extending from this motif. Histone amino-terminal tails pass over and between the gyres of the DNA superhelix to contact neighbouring particles. The lack of uniformity between multiple histone/DNA-binding sites causes the DNA to deviate from ideal superhelix geometry.
- Thatcher TH, Gorovsky MA
- Phylogenetic analysis of the core histones H2A, H2B, H3, and H4.
- Nucleic Acids Res. 1994; 22: 174-9
- Display abstract
- Despite the ubiquity of histones in eukaryotes and their important role in determining the structure and function of chromatin, no detailed studies of the evolution of the histones have been reported. We have constructed phylogenetic trees for the core histones H2A, H2B, H3, and H4. Histones which form dimers (H2A/H2B and H3/H4) have very similar trees and appear to have co-evolved, with the exception of the divergent sea urchin testis H2Bs, for which no corresponding divergent H2As have been identified. The trees for H2A and H2B also support the theory that animals and fungi have a common ancestor. H3 and H4 are 10-fold less divergent than H2A and H2B. Three evolutionary histories are observed for histone variants. H2A.F/Z-type variants arose once early in evolution, while H2A.X variants arose separately, during the evolution of multicellular animals. H3.3-type variants have arisen in multiple independent events.
Structure (3D structures containing this domain)

3D Structures of H3 domains in PDB

PDB code	Main view	Title
1aoi		Complex between nucleosome core particle (h3,h4,h2a,h2b) and 146 bp long dna fragment
1eqz		X-ray structure of the nucleosome core particle at 2.5 a resolution
1f66		2.6 a crystal structure of a nucleosome core particle containing the variant histone h2a.z
1hio		Histone octamer (chicken), chromosomal protein, alpha carbons only
1hq3		Crystal structure of the histone-core-octamer in kcl/phosphate
1id3		Crystal structure of the yeast nucleosome core particle reveals fundamental differences in inter-nucleosome interactions
1kx3		X-ray structure of the nucleosome core particle, ncp146, at 2.0 a resolution
1kx4		X-ray structure of the nucleosome core particle, ncp146b, at 2.6 a resolution
1kx5		X-ray structure of the nucleosome core particle, ncp147, at 1.9 a resolution
1m18		Ligand binding alters the structure and dynamics of nucleosomal dna
1m19		Ligand binding alters the structure and dynamics of nucleosomal dna
1m1a		Ligand binding alters the structure and dynamics of nucleosomal dna
1p34		Crystallographic studies of nucleosome core particles containing histone 'sin' mutants
1p3a		Crystallographic studies of nucleosome core particles containing histone 'sin' mutants
1p3b		Crystallographic studies of nucleosome core particles containing histone 'sin' mutants
1p3f		Crystallographic studies of nucleosome core particles containing histone 'sin' mutants
1p3g		Crystallographic studies of nucleosome core particles containing histone 'sin' mutants
1p3i		Crystallographic studies of nucleosome core particles containing histone 'sin' mutants
1p3k		Crystallographic studies of nucleosome core particles containing histone 'sin' mutants
1p3l		Crystallographic studies of nucleosome core particles containing histone 'sin' mutants
1p3m		Crystallographic studies of nucleosome core particles containing histone 'sin' mutants
1p3o		Crystallographic studies of nucleosome core particles containing histone 'sin' mutants
1p3p		Crystallographic studies of nucleosome core particles containing histone 'sin' mutants
1s32		Molecular recognition of the nucleosomal 'supergroove'
1tzy		Crystal structure of the core-histone octamer to 1.90 angstrom resolution
1u35		Crystal structure of the nucleosome core particle containing the histone domain of macroh2a
1zbb		Structure of the 4_601_167 tetranucleosome
1zla		X-ray structure of a kaposi's sarcoma herpesvirus lana peptide bound to the nucleosomal core
2aro		Crystal structure of the native histone octamer to 2.1 angstrom resolution, crystalised in the presence of s- nitrosoglutathione
2cv5		Crystal structure of human nucleosome core particle
2f8n		2.9 angstrom x-ray structure of hybrid macroh2a nucleosomes
2fj7		Crystal structure of nucleosome core particle containing a poly (da.dt) sequence element
2hio		Histone octamer (chicken), chromosomal protein
2hue		Structure of the h3-h4 chaperone asf1 bound to histones h3 and h4
2io5		Crystal structure of the cia- histone h3-h4 complex
2nqb		Drosophila nucleosome structure
2nzd		Nucleosome core particle containing 145 bp of dna
2pyo		Drosophila nucleosome core
3b6f		Nucleosome core particle treated with cisplatin
3b6g		Nucleosome core particle treated with oxaliplatin
3c1b		The effect of h3 k79 dimethylation and h4 k20 trimethylation on nucleosome and chromatin structure
3c1c		The effect of h3 k79 dimethylation and h4 k20 trimethylation on nucleosome and chromatin structure
3c9k		Model of histone octamer tubular crystals

Links (links to other resources describing this domain)
PFAM histone
INTERPRO IPR000164
PROSITE HISTONE_H3_2

PFAM	histone
INTERPRO	IPR000164
PROSITE	HISTONE_H3_2