SNAP output for PDB entry 6dzt [SNAP web server]

PDB-id

6dzt; SNAP-derived features in text and JSON formats; DNAproDB

Class

nuclear protein

Method

cryo-EM (2.99 Å)

Summary

cryo-EM structure of nucleosome in complex with a single chain antibody fragment

Reference

Zhou BR, Yadav KNS, Borgnia M, Hong J, Cao B, Olins AL, Olins DE, Bai Y, Zhang P (2019): "Atomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided by an antibody fragment." Nat Commun, 10, 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.