6O1D

Cryo-EM structure of the centromeric nucleosome with native alpha satellite DNA

Summary for 6O1D

• Entry DOI: 10.2210/pdb6o1d/pdb
• EMDB information: 0586 8938 8945 8949
• Descriptor: Histone H3-like centromeric protein A, Histone H4, Histone H2A type 1-B/E, ... (6 entities in total)
• Functional Keywords: cenp-a, centromere, native alpha satellite dna, nucleosome, nuclear protein
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 10
• Total formula weight: 204556.40

Authors

Zhou, B.-R. (deposition date: 2019-02-19, release date: 2019-05-22, Last modification date: 2024-03-20)

Primary citation

Zhou, B.R.,Yadav, K.N.S.,Borgnia, M.,Hong, J.,Cao, B.,Olins, A.L.,Olins, D.E.,Bai, Y.,Zhang, P.
Atomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided by an antibody fragment.
Nat Commun, 10:2301-2301, 2019

PubMed Abstract: Genomic DNA in eukaryotes is organized into chromatin through association with core histones to form nucleosomes, each distinguished by their DNA sequences and histone variants. Here, we used a single-chain antibody fragment (scFv) derived from the anti-nucleosome antibody mAb PL2-6 to stabilize human CENP-A nucleosome containing a native α-satellite DNA and solved its structure by the cryo-electron microscopy (cryo-EM) to 2.6 Å resolution. In comparison, the corresponding cryo-EM structure of the free CENP-A nucleosome could only reach 3.4 Å resolution. We find that scFv binds to a conserved acidic patch on the histone H2A-H2B dimer without perturbing the nucleosome structure. Our results provide an atomic resolution cryo-EM structure of a nucleosome and insight into the structure and function of the CENP-A nucleosome. The scFv approach is applicable to the structural determination of other native-like nucleosomes with distinct DNA sequences.

PubMed: 31127102
DOI: 10.1038/s41467-019-10247-4

Experimental method

ELECTRON MICROSCOPY (3.395 Å)