H2BHistone H2B |
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| SMART accession number: | SM00427 |
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| Description: | |
| Interpro abstract (IPR000558): | Histone H2B is one of the four histones, along with H2A, H3 and H4, which forms the eukaryotic nucleosome core. Histone H2B is a small, highly conserved nuclear protein that, together with 2 molecules each of histones H2A, H3 and H4, forms the eukaryotic nucleosome core [(PUBMED:2041803)]; the nucleosome octamer winds ~146 DNA base-pairs. |
| GO process: | nucleosome assembly (GO:0006334) |
| GO component: | nucleus (GO:0005634), nucleosome (GO:0000786) |
| GO function: | DNA binding (GO:0003677) |
| Family alignment: |
There are 774 H2B domains in 773 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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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)
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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 H2B 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 2jss 
Nmr structure of chaperone chz1 complexed with histone h2a.z-h2b 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)
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PFAM histone INTERPRO IPR000558 PROSITE HISTONE_H2B