General Information

Database accession: MF2210001

Name: H2A-H2B histone dimer (Xenopus laevis), containing histone variants H2A type 1 and H2B 1.1

PDB ID: 1aoi PDB

Experimental method: X-ray (2.80 Å)

Assembly: heterodimer

Source organism: Xenopus laevis

Primer publication of the structure:

Luger K, M├Ąder AW, Richmond RK, Sargent DF, Richmond TJ
Crystal structure of the nucleosome core particle at 2.8 A resolution.

(1997) Nature 389: 251-60

PMID: 9305837 PubMed

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.


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 type 1

Source organism: Xenopus laevis

Length: 116 residues

Sequence:Sequence according to PDB SEQRESGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK

UniProtKB AC: P06897 (positions: 5-120) UniProt Coverage: 89.2%

UniRef90 AC: UniRef90_Q00728 (positions: 6-120) UniRef90

Chain D

Name: Histone H2B 1.1

Source organism: Xenopus laevis

Length: 99 residues

Sequence:Sequence according to PDB SEQRESKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

UniProtKB AC: P02281 (positions: 28-126) UniProt Coverage: 78.6%

UniRef90 AC: UniRef90_P57053 (positions: 28-126) 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).

There are 69 related structures in the Protein Data Bank:





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