3X1V image
Deposition Date 2014-11-28
Release Date 2015-09-23
Last Version Date 2023-11-08
Entry Detail
PDB ID:
3X1V
Title:
Crystal structure of nucleosome core particle in the presence of histone variant involved in reprogramming
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Mus musculus (Taxon ID: 10090)
synthetic (Taxon ID: 32630)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.92 Å
R-Value Free:
0.25
R-Value Work:
0.19
R-Value Observed:
0.19
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:135
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:102
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1-B/E
Gene (Uniprot):H2AC4, H2AC8
Chain IDs:E (auth: C), I (auth: G)
Chain Length:129
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Histone H2B type 1-A
Gene (Uniprot):H2bc1
Chain IDs:F (auth: D), J (auth: H)
Chain Length:126
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (146-MER)
Chain IDs:A (auth: I), B (auth: J)
Chain Length:146
Number of Molecules:2
Biological Source:synthetic
Primary Citation
Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming
Biochem.Biophys.Res.Commun. 464 929 935 (2015)
PMID: 26188507 DOI: 10.1016/j.bbrc.2015.07.070

Abstact

Histone variants TH2a and TH2b are highly expressed in testes, oocytes and zygotes. Our recent analysis suggested that these histone variants enhance the induced generation of pluripotent stem cells (iPSCs) when co-expressed along with four transcription factors, Oct3/4, Sox2, Klf4 and c-Myc (OSKM), and are associated with an open chromatin structure [1]. In the present study, we report the crystal structures of nucleosomes (NCPs) with the mouse histone variants, TH2a and TH2b. The structures revealed two significant changes, as compared to the canonical counterparts: fewer histone-DNA contacts and changes in dimer-dimer interactions between TH2a-TH2a' (L1-loop). In vivo studies with domain swapping and point mutants of the variants revealed that the residues in the histone tails and the TH2a-L1 loop are important for reprogramming. Taken together, our work indicates that the NCP variants with structural modifications and flexible tails are most likely important for enhanced reprogramming of functions.

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