Document Type


Publication Date



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.


Originally published:
Bing-Rui Zhou, Sathish Yadav, ,K.N., Borgnia, M., Hong, J., Cao, B., Olins, A. L., . . . Zhang, P. (2019). Atomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided by an antibody fragment. Nature Communications, 10, 1-7. doi:

© 2019 The Authors. This work is published under (the “License”).

Supplementary materials descriptions:
1: Supplementary Figures: 1 – 14, Supplementary Table 1
2: Supplementary Movie: Cryo-EM map and structural features of human CENP-A nucleosome bound to the scFv.

AtomicResolutionCryoEMsupplemental1.pdf (9476 kB)
Supplementary file 1 (.pdf)

AtomicResolutionCryoEMsupplemental2.mp4 (13056 kB)
Supplementary file 2 (.mp4)



To view the content in your browser, please download Adobe Reader or, alternately,
you may Download the file to your hard drive.

NOTE: The latest versions of Adobe Reader do not support viewing PDF files within Firefox on Mac OS and if you are using a modern (Intel) Mac, there is no official plugin for viewing PDF files within the browser window.