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Structural basis for TRF2-RAP1 recruitment by EBNA1 at the EBV origin of replication
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  • Published: 09 April 2026

Structural basis for TRF2-RAP1 recruitment by EBNA1 at the EBV origin of replication

  • Samantha Sustek1,2,
  • Troy E. Messick2,
  • Jayaraju Dheekollu2,
  • Coltin Albitz2,
  • Christopher Chen2,
  • Anneliese Faustino2,
  • Hsin-Yao Tang2,
  • Hee Jong Kim1,
  • Kenji Murakami1 &
  • …
  • Paul M. Lieberman2 

Scientific Reports , Article number:  (2026) Cite this article

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Subjects

  • Biochemistry
  • Biophysics
  • Cell biology
  • Microbiology
  • Molecular biology
  • Structural biology

Abstract

Epstein-Barr Nuclear Antigen 1 (EBNA1) is essential for the episomal maintenance and DNA replication of Epstein-Barr virus (EBV) in latently infected cells and acts through binding to oriP. The minimal replicative unit of oriP (½DS) contains four EBNA1 binding sites flanked by single telomeric nonamers that recruit shelterin proteins TRF2 and Rap1, but the structural basis for host-factor engagement is not known. Here, we integrate cryo-electron microscopy, zero-length cross-linking mass spectrometry, Alphafold3 modeling, and biochemical binding assays to define the complex formed by EBNA1-TRF2-Rap1 assembly on the ½DS. We find that a highly dynamic complex is formed, with the TRF2 homodimerization domain (TRFH) flexibly interacting with EBNA1 on the surface opposite the DNA-binding region, where there is a large acidic patch in EBNA1 that is unique amongst the herpesvirus episome maintenance proteins. Mutagenesis of this acidic patch abolishes TRFH binding and oriP-dependent plasmid replication. These findings identify a previously uncharacterized acidic patch docking surface on EBNA1 essential for coordinating TRF2-Rap1 at oriP and provide new insights into both EBV and telomere DNA replication.

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Data availability

The datasets generated during the current study are available in the Supplementary Materials and at https://www.ebi.ac.uk/emdb/EMD-73305 for Cryo-EM data and at https://proteomecentral.proteomexchange.org/cgi/GetDataset? ID=PXD068321.

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Acknowledgements

We thank members of the Electron Microscopy Resource Lab (EMRL) and the Beckman Center for Cryo-EM at the University of Pennsylvania for cryo-EM screening and grid clipping. We thank the University of Pennsylvania institute for Structural Biology (ISB) and Jesper Pallesen at the Wistar Institute for advice on cryo-EM methodology and analyses. This research was, in part, supported by the National Cancer Institute’s National Cryo-EM Facility at the Frederick National Laboratory for Cancer Research under contract 75N91019D00024. This work was supported by grants from the NIH R01 CA140652 and R01 CA093606 to PML, R01 CA259171 to TEM, and NIH R01GM123233 to KM. This work was also supported by an Institutional Core grant to the Wistar Institute Cancer Center P30 CA010815.

Funding

This research was, in part, supported by the National Cancer Institute’s National Cryo-EM Facility at the Frederick National Laboratory for Cancer Research under contract 75N91019D00024. This work was supported by grants from the NIH R01 CA140652 and R01 CA093606 to PML, R01 CA259171 to TEM, and NIH R01GM123233 to KM. This work was also supported by an Institutional Core grant to the Wistar Institute Cancer Center P30 CA010815.

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Authors and Affiliations

  1. Department of Biochemistry and Biophysics, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, 19104, USA

    Samantha Sustek, Hee Jong Kim & Kenji Murakami

  2. The Wistar Institute, Philadelphia, PA, 19104, USA

    Samantha Sustek, Troy E. Messick, Jayaraju Dheekollu, Coltin Albitz, Christopher Chen, Anneliese Faustino, Hsin-Yao Tang & Paul M. Lieberman

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Contributions

SS wrote the main manuscript text, prepared figures, and performed all EMSA experiments, mass photometry, cryo-EM sample preparation and data analysis, and Alphafold3 modeling. TM expressed and purified proteins, assisted with all structural work, and assisted with manuscript edits. JD and CA performed replication assay experiments. CC performed cyclohexamide chase experiments. AF and HYT performed crosslinking mass spectrometry experiments. HJK and KM assisted with cryo-EM data analysis and provided resources. PML supervised the project and assisted with manuscript edits and provided resources. All authors discussed the results and contributed to the final manuscript.

Corresponding authors

Correspondence to Kenji Murakami or Paul M. Lieberman.

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Competing interests

PML is a founder of Vironika LLC and is listed on patents relating to EBNA1 inhibitors. PML has served on advisory panels for Pfizer, GSK, Sanofi, Merck, and Moderna.

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Sustek, S., Messick, T.E., Dheekollu, J. et al. Structural basis for TRF2-RAP1 recruitment by EBNA1 at the EBV origin of replication. Sci Rep (2026). https://doi.org/10.1038/s41598-026-43067-w

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  • Received: 19 December 2025

  • Accepted: 28 February 2026

  • Published: 09 April 2026

  • DOI: https://doi.org/10.1038/s41598-026-43067-w

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Keywords

  • EBV
  • EBNA1
  • Shelterin
  • TRF2
  • hRAP1
  • TERF2
  • TERF2IP
  • CryoEM
  • oriP
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