9PI5

Poly dA bound form of Single stranded DNA-binding protein(ICP8) from Herpes simplex virus-1. Mutations: C254S, C455S

Summary for 9PI5

• Entry DOI: 10.2210/pdb9pi5/pdb
• Descriptor: Major DNA-binding protein, DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3') (2 entities in total)
• Functional Keywords: single-stranded dna binding protein, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Human alphaherpesvirus 1 (Herpes simplex virus type 1); More
• Total number of polymer chains: 2
• Total formula weight: 123760.35

Authors

Erlandsen, H.,Wright, D. (deposition date: 2025-07-10, release date: 2026-04-15, Last modification date: 2026-05-20)

Primary citation

Erlandsen, H.,Krucinska, J.,Wilderman, P.R.,Makkay, A.M.,Szczepaniak, R.,Wright, L.R.,Weller, S.K.,Wright, D.L.
The crystal structure of the herpes virus ICP8 protein in complex with single-stranded DNA reveals the molecular determinants of nucleotide recognition.
J.Biol.Chem., 302:111366-111366, 2026

PubMed Abstract: The HSV-1 single-strand annealing protein ICP8 (UL29) is essential for viral DNA replication and recombination. Although its overall architecture has been described, the molecular basis of single-stranded DNA (ssDNA) recognition was unknown. We report crystal structures of C-terminally truncated ICP8 (ICP8Δ60) bound to poly(dT)25 or poly(dA)25 ssDNA at 3.0-3.1 Å resolution, along with higher-resolution apo structures of surface-entropy-reduction variants. ssDNA binds within the neck region between the head and shoulder domains, contacting conserved OB-fold residues via base-specific hydrogen bonds, π-stacking and phosphate backbone interactions. In the poly(dT)25 complex, coordination of a Zn ion stabilizes the zinc finger motif; whereas, in the poly(dA)25 complex, Zn displacement promotes disulfide bond formation that effectively locks the protein into an altered conformation. Microscale thermophoresis and label-free differential scanning fluorimetry reveal a strong preference for pyrimidine-rich sequences, with nanomolar affinity for poly(dT)25 and micromolar for poly(dA)25. Structural modeling identified Y543, R576, R772, R793, Y988, and F998 as key DNA-contact residues. Alanine substitutions caused severe replication defects, particularly for R772A, Y988A, and F998A. ssDNA binding induces ∼26 Å displacement and ∼35 degree rotation of the C-terminal domain and ordering of flexible loops, suggesting a mechanism for cooperative filament assembly. These structures define the molecular determinants of ICP8-ssDNA recognition, reveal thymidine bias and provide a framework for targeting ICP8-mediated functions in herpesvirus replication.

PubMed: 41833734
DOI: 10.1016/j.jbc.2026.111366

Experimental method

X-RAY DIFFRACTION (3 Å)