3X1U: Crystal structure of nucleosome core particle in the presence of histone variants involved in reprogramming

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.
PDB ID: 3X1UDownload
MMDB ID: 132754
PDB Deposition Date: 2014/11/28
Updated in MMDB: 2017/12
Experimental Method:
x-ray diffraction
Resolution: 3.25  Å
Source Organism:
Mus musculus
Similar Structures:
Biological Unit for 3X1U: decameric; determined by author and by software (PISA)
Molecular Components in 3X1U
Label Count Molecule
Proteins (8 molecules)
Histone H3.1(Gene symbol: HIST1H3A)
Molecule annotation
Histone H4(Gene symbol: HIST1H4I)
Molecule annotation
Histone H2A
Molecule annotation
Histone H2B Type 1-B(Gene symbol: HIST1H2BB)
Molecule annotation
Nucleotide(1 molecule)
DNA (146-mer)
Molecule annotation
Chemicals (10 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB