9LN8

Structure of NAP1 in complex with H2A.Z-H2B

Summary for 9LN8

• Entry DOI: 10.2210/pdb9ln8/pdb
• Descriptor: Nucleosome assembly protein 1-like 1, H2A.Z-H2B (2 entities in total)
• Functional Keywords: nap1, h2a-h2b, h3-h4, histone chaperone, nucleosome, h2a.z, chaperone
• Biological source: Caenorhabditis elegans; More
• Total number of polymer chains: 3
• Total formula weight: 92459.44

Authors

Li, X.,Li, X. (deposition date: 2025-01-21, release date: 2025-12-24, Last modification date: 2026-02-11)

Primary citation

Xu, L.,Zhang, J.,Wang, Y.,Liu, D.,Zeng, C.,Chen, J.,Pan, X.
Structural insights into H2A-H2B and H2A.Z-H2B sliding on histone chaperone NAP1.
Acta Biochim.Biophys.Sin., 2025

PubMed Abstract: The evolutionarily conserved nucleosome assembly protein 1 (NAP1) functions as a histone chaperone for H2A-H2B, regulating nucleosome assembly and maintaining chromatin integrity. However, the dynamic and variable nature of the interactions between acidic NAP1 and basic H2A-H2B has obscured the molecular basis of its chaperoning activity. Here, we report the crystal structures of NAP1 (CeNAP1) in complex with H2A-H2B (XlH2A-H2B) and with . H2A.Z-H2B (CeH2A.Z-H2B) at 3.35 Å and 2.8 Å, respectively. In our structures, H2A/H2A.Z-H2B binds to the acidic concave surface of CeNAP1 in three distinct poses, with two in the CeNAP1-XlH2A-H2B complex and one in the CeNAP1-CeH2A.Z-H2B complex. These poses are different from the two poses observed in the previously reported CeNAP1-CeH2A/H2A.Z-H2B structures. The predominant interaction involves engagement of the acidic CeNAP1 α6-carboxy-terminal (C-terminal) tail by the basic H2A/H2A.Z αN-α1 region, stabilized by salt bridges and electrostatic interactions. A comparative analysis of all five known poses reveals that H2A/H2A.Z-H2B can shift approximately 20.7 Å along the α6-C-terminal tail-C'-terminal tail-α6' axis. These findings demonstrate a sliding binding mode of H2A/H2A.Z-H2B on NAP1, providing new mechanistic insights into nucleosome assembly activity of histone chaperones.

PubMed: 41403246
DOI: 10.3724/abbs.2025241

Experimental method

X-RAY DIFFRACTION (2.8 Å)