5WCU

Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5

Summary for 5WCU

• Entry DOI: 10.2210/pdb5wcu/pdb
• Descriptor: Histone H3, Histone H4, Histone H2A, ... (7 entities in total)
• Functional Keywords: nucleosome core particle, histone fold, chromosome, chromatin, globular domain, histone h5, gh5, 167 bp nucleosome, chromatosome, nucleosome packing, 30 nm chromatin fiber, linker histone h5, linker dna, nucleosome binding protein, protein dna complexes, dna binding, chromatin higher order structure, chromatin folding, chromatin binding protein-dna complex, chromatin binding protein/dna
• Biological source: Drosophila melanogaster (Fruit fly); More
• Total number of polymer chains: 22
• Total formula weight: 393467.21

Authors

Jiang, J.S.,Zhou, B.R. (deposition date: 2017-07-02, release date: 2018-10-31, Last modification date: 2023-10-04)

Primary citation

Zhou, B.R.,Jiang, J.,Ghirlando, R.,Norouzi, D.,Sathish Yadav, K.N.,Feng, H.,Wang, R.,Zhang, P.,Zhurkin, V.,Bai, Y.
Revisit of Reconstituted 30-nm Nucleosome Arrays Reveals an Ensemble of Dynamic Structures.
J. Mol. Biol., 430:3093-3110, 2018

PubMed Abstract: It has long been suggested that chromatin may form a fiber with a diameter of ~30 nm that suppresses transcription. Despite nearly four decades of study, the structural nature of the 30-nm chromatin fiber and conclusive evidence of its existence in vivo remain elusive. The key support for the existence of specific 30-nm chromatin fiber structures is based on the determination of the structures of reconstituted nucleosome arrays using X-ray crystallography and single-particle cryo-electron microscopy coupled with glutaraldehyde chemical cross-linking. Here we report the characterization of these nucleosome arrays in solution using analytical ultracentrifugation, NMR, and small-angle X-ray scattering. We found that the physical properties of these nucleosome arrays in solution are not consistent with formation of just a few discrete structures of nucleosome arrays. In addition, we obtained a crystal of the nucleosome in complex with the globular domain of linker histone H5 that shows a new form of nucleosome packing and suggests a plausible alternative compact conformation for nucleosome arrays. Taken together, our results challenge the key evidence for the existence of a limited number of structures of reconstituted nucleosome arrays in solution by revealing that the reconstituted nucleosome arrays are actually best described as an ensemble of various conformations with a zigzagged arrangement of nucleosomes. Our finding has implications for understanding the structure and function of chromatin in vivo.

PubMed: 29959925
DOI: 10.1016/j.jmb.2018.06.020

Experimental method

X-RAY DIFFRACTION (5.53 Å)