Atomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided by an antibody fragment

Nat Commun. 2019 May 24;10(1):2301. doi: 10.1038/s41467-019-10247-4.

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.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Centromere Protein A / immunology
  • Centromere Protein A / metabolism
  • Centromere Protein A / ultrastructure*
  • Cryoelectron Microscopy
  • DNA, Satellite / metabolism
  • DNA, Satellite / ultrastructure*
  • Histones / metabolism
  • Histones / ultrastructure
  • Models, Molecular
  • Nucleosomes / metabolism
  • Nucleosomes / ultrastructure*
  • Single-Chain Antibodies / immunology
  • Single-Chain Antibodies / metabolism
  • Single-Chain Antibodies / ultrastructure

Substances

  • CENPA protein, human
  • Centromere Protein A
  • DNA, Satellite
  • Histones
  • Nucleosomes
  • Single-Chain Antibodies