General Information

Database accession: MF2211001

Name: H2A-H2B histone dimer (human/Xenopus laevis), containing histone variants H2A.Z and H2B 1.1

PDB ID: 1f66 PDB

Experimental method: X-ray (2.60 Å)

Assembly: heterodimer

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

PMID: 11101893 PubMed

Abstract:

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.

Function and Biology Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.

Molecular function:

DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GeneOntology

protein heterodimerization activity Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer. GeneOntology

Biological process: not assigned

Cellular component:

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. GeneOntology

nucleosome A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures. GeneOntology

Structure Summary Structural annotations of the participating protein chains.

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

Chain C

Name: Histone H2A.Z

Source organism: Mus musculus

Length: 128 residues

Sequence:Sequence according to PDB SEQRESMAGGKAGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKSLIGKKGQQKTV

UniProtKB AC: P0C0S6 (positions: 1-128) UniProt Coverage: 100%

UniRef90 AC: UniRef90_P0C0S5 (positions: 1-128) UniRef90

Chain D

Name: Histone H2B 1.1

Source organism: Xenopus laevis

Length: 126 residues

Sequence:Sequence according to PDB SEQRESMPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

UniProtKB AC: P02281 (positions: 1-126) UniProt Coverage: 100%

UniRef90 AC: UniRef90_P57053 (positions: 1-126) UniRef90

Evidence Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding.

Complex evidence:

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).

Related Structure(s) Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap).

No related structure was found in the Protein Data Bank.

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