|SMART accession number:||SM00417|
|Interpro abstract (IPR001951):||Histone H4 is one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core. Along with H3, it plays a central role in nucleosome formation. The sequence of histone H4 has remained almost invariant in more then 2 billion years of evolution [(PUBMED:8121801), (PUBMED:6808351), (PUBMED:3340182)].|
|GO process:||nucleosome assembly (GO:0006334)|
|GO component:||nucleus (GO:0005634), nucleosome (GO:0000786)|
|GO function:||DNA binding (GO:0003677)|
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- 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 H4 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.
- Burley SK, Xie X, Clark KL, Shu F
- Histone-like transcription factors in eukaryotes.
- Curr Opin Struct Biol. 1997; 7: 94-102
- Display abstract
Histone proteins have long been recognized as important regulators of eukaryotic gene expression. Condensation of DNA into chromatin by the core (H2A, H2B, H3, H4) and linker (H1, H5) histones effectively represses transcription initiation from the promoters of genes that have been packaged. Recently, eukaryotic transcriptional activators and coactivators (both positive and negative) resembling core and linker histone proteins have been discovered. Substantial progress has been made on structural and mechanistic studies of histones and histone-like transcription factors. Three-dimensional structures solved include the core histone octamer, an archael histone homodimer, two core histone-like subunits of transcription factor IID, a linker histone, and a linker histone-like transcriptional activator.
- 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.
- Ebralidse KK, Grachev SA, Mirzabekov AD
- A highly basic histone H4 domain bound to the sharply bent region of nucleosomal DNA.
- Nature. 1988; 331: 365-7
- Display abstract
A nucleosomal core particle is composed of two each of histones H2A, H2B, H3 and H4 located inside the particle with approximately 47 base pairs (bp) of DNA wrapped around the octamer in about 1.8 turns of a left-handed superhelix. The path of the superhelix is not smooth; the DNA is sharply bent, or kinked, at positions symmetrically disposed at a distance of about one and four double-helical turns in both directions from the nucleosomal dyad axis (designated as sites +/- 1 and +/- 4 respectively). This non-uniform bending is considered archetypal to other DNA-protein complexes, but its mechanism is not clear (reviewed in ref. 4). DNA-histone chemical cross-linking within the core particle has revealed strong binding of each of the two histone H4 molecules to DNA at a distance of 1.5 helical turns either side of the nucleosomal dyad axis (sites +/- 1.5). In each of these sites, a single flexible domain of H4 was previously shown to contact three points, at about nucleotides 55 and 65 on one strand and nucleotide 88 on the complementary strand, numbering from the 5' terminus of each 147-base strand; these three locations are closely juxtaposed across the highly compressed minor and major grooves (Fig. 1). Here we report that the amino-acid residue of histone H4 cross-linked at the 1.5 site is histidine-18, embedded in a highly basic cluster Lys-Arg-His-Arg-Lys-Val-Leu-Arg which is probably involved in the sharp bending of the DNA double helix at the +/- 1 sites.
- Structure (3D structures containing this domain)
3D Structures of H4 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 IPR001951 PROSITE HISTONE_H4