EMD-22790

Single-particle
3.38 Å
EMD-22790 Deposition: 02/10/2020
Map released: 15/09/2021
Last modified: 29/05/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-22790

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

EMD-22790

Single-particle
3.38 Å
EMD-22790 Deposition: 02/10/2020
Map released: 15/09/2021
Last modified: 29/05/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Xenopus laevis
Sample: Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction)
Fitted models: 7kbd (Avg. Q-score: 0.489)
Raw data: EMPIAR-10692

Deposition Authors: Arimura Y , Funabiki H
Structural features of nucleosomes in interphase and metaphase chromosomes.
Arimura Y , Shih RM , Froom R , Funabiki H
(2021) Mol Cell , 81 , 4377
PUBMED: 34478647
DOI: doi:10.1016/j.molcel.2021.08.010
ISSN: 1097-2765
ASTM: MOCEFL
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.