7KBD

Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction)

Summary for 7KBD

• Entry DOI: 10.2210/pdb7kbd/pdb
• EMDB information: 22790
• Descriptor: Histone H3.2, Histone H4, Histone H2A, ... (6 entities in total)
• Functional Keywords: nucleosome, interphase, cell cycle, chromatin, dna binding protein, structural protein-dna complex, structural protein/dna
• Biological source: Xenopus laevis (African clawed frog); More
• Total number of polymer chains: 10
• Total formula weight: 204531.34

Authors

Arimura, Y.,Funabiki, H. (deposition date: 2020-10-02, release date: 2021-09-15, Last modification date: 2024-05-29)

Primary citation

Arimura, Y.,Shih, R.M.,Froom, R.,Funabiki, H.
Structural features of nucleosomes in interphase and metaphase chromosomes.
Mol.Cell, 81:4377-, 2021

PubMed Abstract: Structural heterogeneity of nucleosomes in functional chromosomes is unknown. Here, we devise the template-, reference- and selection-free (TRSF) cryo-EM pipeline to simultaneously reconstruct cryo-EM structures of protein complexes from interphase or metaphase chromosomes. The reconstructed interphase and metaphase nucleosome structures are on average indistinguishable from canonical nucleosome structures, despite DNA sequence heterogeneity, cell-cycle-specific posttranslational modifications, and interacting proteins. Nucleosome structures determined by a decoy-classifying method and structure variability analyses reveal the nucleosome structural variations in linker DNA, histone tails, and nucleosome core particle configurations, suggesting that the opening of linker DNA, which is correlated with H2A C-terminal tail positioning, is suppressed in chromosomes. High-resolution (3.4-3.5 Å) nucleosome structures indicate DNA-sequence-independent stabilization of superhelical locations ±0-1 and ±3.5-4.5. The linker histone H1.8 preferentially binds to metaphase chromatin, from which chromatosome cryo-EM structures with H1.8 at the on-dyad position are reconstituted. This study presents the structural characteristics of nucleosomes in chromosomes.

PubMed: 34478647
DOI: 10.1016/j.molcel.2021.08.010

Experimental method

ELECTRON MICROSCOPY (3.38 Å)