5Y0C image
Entry Detail
PDB ID:
5Y0C
Title:
Crystal Structure of the human nucleosome at 2.09 angstrom resolution
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2017-07-16
Release Date:
2018-07-18
Method Details:
Experimental Method:
Resolution:
2.09 Å
R-Value Free:
0.24
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Histone H3.1
Chain IDs:C (auth: A), G (auth: E)
Chain Length:139
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Histone H4
Chain IDs:D (auth: B), H (auth: F)
Chain Length:106
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Histone H2A type 1-B/E
Chain IDs:E (auth: C), I (auth: G)
Chain Length:133
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Histone H2B type 1-J
Chain IDs:F (auth: D), J (auth: H)
Chain Length:129
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Description:DNA (146-MER)
Chain IDs:A (auth: I), B (auth: J)
Chain Length:146
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome.
Nucleic Acids Res. 46 10007 10018 (2018)
PMID: 30053102 DOI: 10.1093/nar/gky661

Abstact

Mutations of the Glu76 residue of canonical histone H2B are frequently found in cancer cells. However, it is quite mysterious how a single amino acid substitution in one of the multiple H2B genes affects cell fate. Here we found that the H2B E76K mutation, in which Glu76 is replaced by Lys (E76K), distorted the interface between H2B and H4 in the nucleosome, as revealed by the crystal structure and induced nucleosome instability in vivo and in vitro. Exogenous production of the H2B E76K mutant robustly enhanced the colony formation ability of the expressing cells, indicating that the H2B E76K mutant has the potential to promote oncogenic transformation in the presence of wild-type H2B. We found that other cancer-associated mutations of histones, H3.1 E97K and H2A.Z.1 R80C, also induced nucleosome instability. Interestingly, like the H2B E76K mutant, the H3.1 E97K mutant was minimally incorporated into chromatin in cells, but it enhanced the colony formation ability. In contrast, the H2A.Z.1 R80C mutant was incorporated into chromatin in cells, and had minor effects on the colony formation ability of the cells. These characteristics of histones with cancer-associated mutations may provide important information toward understanding how the mutations promote cancer progression.

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