9LRW

Cryo-EM structure of Fission yeast centromeric nucleosome Class 2

Summary for 9LRW

• Entry DOI: 10.2210/pdb9lrw/pdb
• EMDB information: 63345
• Descriptor: Histone H3-like centromeric protein cnp1, Histone H4, Histone H2A-alpha, ... (6 entities in total)
• Functional Keywords: nucleosome dynamics, cenp-a, cnp1, kinetochore assembly, chromosome segregation, nuclear protein/dna, nuclear protein-dna complex
• Biological source: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (fission yeast); More
• Total number of polymer chains: 10
• Total formula weight: 196960.12

Authors

Xiong, Y.,Zang, J. (deposition date: 2025-02-01, release date: 2026-02-04)

Primary citation

Xiong, Y.,Jian, Y.,Zhang, Y.,Zhang, M.,Zhang, X.,Zhang, K.,Fu, C.,Tian, T.,Zang, J.
Cnp1 N-terminal dynamics regulate L1 loop recognition by Mis15 to orchestrate kinetochore assembly in Schizosaccharomyces pombe.
J Mol Cell Biol, 2025

PubMed Abstract: Centromeres are defined by the histone H3 variant CENP-A, which serve as the foundation for kinetochore assembly and ensure faithful chromosome segregation. CENP-A nucleosomes possess distinctive dynamic features, including flexible DNA ends at the entry/exit sites and a mobile N-terminal region, which are properties proposed to facilitate kinetochore assembly, yet the underlying molecular mechanisms remain elusive. Here, we present cryo-electron microscopy structures of Cnp1, the Schizosaccharomyces pombe (S. pombe) ortholog of CENP-A, alone and in complex with Mis15, the fission yeast ortholog of CENP-N. By integrating structural, biochemical, and molecular dynamics analyses, we demonstrate that the N-terminal region of Cnp1 regulates both DNA-end breathing and the conformational mobility of the L1 loop, a critical structural element for Mis15 recognition. Either enhanced dynamics caused by N-terminal deletion or reduced dynamics from targeted residue substitution disrupt Mis15 binding in vitro and impair its centromeric localization in vivo, thereby compromising the earliest steps of constitutive centromere-associated network assembly. Our findings establish the Cnp1 N-terminus as a dynamic allosteric modulator of chromatin architecture and reveal an L1 loop modulation mechanism that links nucleosome flexibility to kinetochore specification and chromosome segregation fidelity in fission yeast.

PubMed: 41453208
DOI: 10.1093/jmcb/mjaf056

Experimental method

ELECTRON MICROSCOPY (3.04 Å)