6KVD image
Deposition Date 2019-09-04
Release Date 2019-12-18
Last Version Date 2023-11-22
Entry Detail
PDB ID:
6KVD
Title:
Crystal structure of human nucleosome containing H2A.J
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.21 Å
R-Value Free:
0.25
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Histone H3.1
Gene (Uniprot):H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12
Chain IDs:C (auth: A), G (auth: E)
Chain Length:139
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Histone H4
Gene (Uniprot):H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16
Chain IDs:D (auth: B), H (auth: F)
Chain Length:106
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Histone H2A.J
Gene (Uniprot):H2AJ
Chain IDs:E (auth: C), I (auth: G)
Chain Length:132
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Histone H2B type 1-J
Gene (Uniprot):H2BC11
Chain IDs:F (auth: D), J (auth: H)
Chain Length:129
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (146-MER)
Chain IDs:A (auth: I), B (auth: J)
Chain Length:146
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Biochemical and structural analyses of the nucleosome containing human histone H2A.J.
J.Biochem. 167 419 427 (2020)
PMID: 31793981 DOI: 10.1093/jb/mvz109

Abstact

Histone H2A.J, a histone H2A variant conserved in mammals, may function in the expression of genes related to inflammation and cell proliferation. In the present study, we purified the human histone H2A.J variant and found that H2A.J is efficiently incorporated into the nucleosome in vitro. H2A.J formed the stable nucleosome, which accommodated the DNA ends. Mutations in the H2A.J-specific residues did not affect the nucleosome stability, although the mutation of the H2A.J Ala40 residue, which is conserved in some members of the canonical H2A class, reduced the nucleosome stability. Consistently, the crystal structure of the H2A.J nucleosome revealed that the H2A.J-specific residues, including the Ala40 residue, did not affect the nucleosome structure. These results provide basic information for understanding the function of the H2A.J nucleosome.

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