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7kbe

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Nucleosome isolated from metaphase chromosome formed in Xenopus egg extract (oligo fraction)

Structural highlights

7kbe is a 10 chain structure with sequence from Xenopus laevis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.5Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

H32_XENLA Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

Publication Abstract from PubMed

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 A) 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.

Structural features of nucleosomes in interphase and metaphase chromosomes.,Arimura Y, Shih RM, Froom R, Funabiki H Mol Cell. 2021 Nov 4;81(21):4377-4397.e12. doi: 10.1016/j.molcel.2021.08.010. , Epub 2021 Sep 2. PMID:34478647^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Arimura Y, Shih RM, Froom R, Funabiki H. Structural features of nucleosomes in interphase and metaphase chromosomes. Mol Cell. 2021 Nov 4;81(21):4377-4397.e12. PMID:34478647 doi:10.1016/j.molcel.2021.08.010