Database accession: MF2211001
Name: H2A-H2B histone dimer (human/Xenopus laevis), containing histone variants H2A.Z and H2B 1.1
PDB ID: 1f66
Experimental method: X-ray (2.60 Å)
Source organism: Mus musculus / Xenopus laevis
Primer publication of the structure:
Suto RK, Clarkson MJ, Tremethick DJ, Luger K
Crystal structure of a nucleosome core particle containing the variant histone H2A.Z.
(2000) Nat. Struct. Biol. 7: 1121-4
Activation of transcription within chromatin has been correlated with the incorporation of the essential histone variant H2A.Z into nucleosomes. H2A.Z and other histone variants may establish structurally distinct chromosomal domains; however, the molecular mechanism by which they function is largely unknown. Here we report the 2.6 A crystal structure of a nucleosome core particle containing the histone variant H2A.Z. The overall structure is similar to that of the previously reported 2.8 A nucleosome structure containing major histone proteins. However, distinct localized changes result in the subtle destabilization of the interaction between the (H2A.Z-H2B) dimer and the (H3-H4)(2) tetramer. Moreover, H2A.Z nucleosomes have an altered surface that includes a metal ion. This altered surface may lead to changes in higher order structure, and/or could result in the association of specific nuclear proteins with H2A.Z. Finally, incorporation of H2A.Z and H2A within the same nucleosome is unlikely, due to significant changes in the interface between the two H2A.Z-H2B dimers.
protein heterodimerization activity Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
Biological process: not assigned
nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
Entry contents: 2 distinct polypeptide molecules
Chains: C, D
Notes: Chains A, B, E, F, G, H, I and J have been removed to highlight the basic interaction that forms the histone dimer composed of chains C and D.
Number of unique protein segments: 2
Name: Histone H2A.Z
Source organism: Mus musculus
Length: 128 residues
Sequence:Sequence according to PDB SEQRESMAGGKAGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKSLIGKKGQQKTV
UniProtKB AC: P0C0S6 (positions: 1-128)Coverage: 100%
UniRef90 AC: UniRef90_P0C0S5 (positions: 1-128)
Name: Histone H2B 1.1
Source organism: Xenopus laevis
Length: 126 residues
Sequence:Sequence according to PDB SEQRESMPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK
UniProtKB AC: P02281 (positions: 1-126)Coverage: 100%
UniRef90 AC: UniRef90_P57053 (positions: 1-126)
Histones form parts of the nucleosome particle by dimerization and subsequent multimerization (PMID: 1946434). The dimer contains both histone subunits in a highly intertwined conformation reflecting the possible domain-swapped origins of the structure (PMID: 17391511). Accordingly, this dimerization has been experimentally characterized to be coupled to the structure formation of both interacting partners (PMID: 12779337); this synergistic folding has been shown separately for H2A-H2B dimers (PMID: 15588829) and H3-H4 dimers as well (PMID: 15096635). Histones containing various types of monomeric subunits can exhibit varying stability and folding kinetics. E.g. in the case of H3-H4 histones, the dimerization is a complex process with the two monomers first adopting an intermediate state upon encounter and then reaching the classical histone fold through restructurization (PMID: 12779337). However, independent of composition and folding kinetics, all histones appear to fold in a cooperative fashion that is coupled to binding (PMID: 11669650).
No related structure was found in the Protein Data Bank.