37XU

Nucleosome containing a nick with a 3'-phosphate and 5'-OH at SHL-5

Summary for 37XU

• Entry DOI: 10.2210/pdb37xu/pdb
• EMDB information: 78608
• Descriptor: Histone H3.2, Histone H4, Histone H2A type 1, ... (7 entities in total)
• Functional Keywords: nucleosome, polynucleotide kinase 3'-phosphatase, dna repair, dna binding protein
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 11
• Total formula weight: 199418.69

Authors

Boesch, D.J.,Evans, J.J.,Weaver, T.M. (deposition date: 2026-08-12, release date: 2026-11-04)

Primary citation

Boesch, D.J.,Martin, N.I.,Evans, J.J.,Weaver, T.M.
Structural basis of end processing in the nucleosome by polynucleotide kinase phosphatase.
Biorxiv, 2026

PubMed Abstract: Genomic DNA is packaged into chromatin through a fundamental repeating unit known as the nucleosome core particle. Chromatinized DNA is under constant assault from endogenous and exogenous sources of damage, which must be effectively repaired to preserve genome stability. Single-strand breaks (SSBs) with chemically heterogeneous DNA ends are one of the most prevalent forms of genomic DNA damage. These SSBs must be enzymatically processed prior to downstream gap-filling DNA synthesis and/or nick ligation during single-strand break repair (SSBR). Polynucleotide kinase phosphatase (PNKP) is a multifunctional end-processing enzyme that possesses two catalytic activities important for converting non-ligatable SSBs into ligatable SSBs. To date, a mechanistic description for how PNKP processes non-ligatable SSBs in the context of chromatin to initiate SSBR remains undefined. Here, we utilize a combination of biochemical assays and cryogenic electron microscopy (cryo-EM) to define the structural basis of end processing in the nucleosome by PNKP. Cryo-EM structures of PNKP engaged with non-ligatable SSBs at three unique positions within the nucleosome reveal that PNKP locally deforms nucleosomal DNA to reposition the SSBs into the kinase and phosphatase active sites, providing a structural basis for the efficient processing of SSBs throughout the nucleosome. Additional cryo-EM structures reveal the PNKP FHA domain also engages the nucleosome acidic patch during non-ligatable SSB recognition, which accelerates the processing of non-ligatable SSBs in the nucleosome. Together, these findings provide important mechanistic insight into the initial end processing step of chromatin-based SSBR.

PubMed: 42845401
DOI: 10.64898/2026.08.12.743989

Experimental method

ELECTRON MICROSCOPY (2.6 Å)