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- EMDB-73305: Cryo-EM structure of the EBV 1/2 DS bound to the EBNA1 DBD, TRF2,... -

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Basic information

Entry
Database: EMDB / ID: EMD-73305
TitleCryo-EM structure of the EBV 1/2 DS bound to the EBNA1 DBD, TRF2, and Rap1
Map data
Sample
  • Complex: Complex of 1/2 DS DNA, EBNA1 DBD (401-607), TRF2, and Rap1
KeywordsEBV / Epstein-Barr virus / oriP / EBNA1 / telomere / shelterin / TRF2 / Rap1 / DNA BINDING PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsSustek S / Messick TE / Murakami K / Lieberman PM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA140652 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA093606 United States
CitationJournal: Sci Rep / Year: 2026
Title: Structural basis for TRF2-RAP1 recruitment by EBNA1 at the EBV origin of replication.
Authors: Samantha Sustek / Troy E Messick / Jayaraju Dheekollu / Coltin Albitz / Christopher Chen / Anneliese Faustino / Hsin-Yao Tang / Hee Jong Kim / Kenji Murakami / Paul M Lieberman /
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 The minimal ...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 The minimal replicative unit of (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 dependent plasmid replication. These findings identify a previously uncharacterized acidic patch docking surface on EBNA1 essential for coordinating TRF2-Rap1 at and provide new insights into both EBV and telomere DNA replication.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-43067-w.
History
DepositionOct 14, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73305.png

Downloads & links

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Map

FileDownload / File: emd_73305.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 128 pix.
= 136.96 Å		1.07 Å/pix.
x 128 pix.
= 136.96 Å		1.07 Å/pix.
x 128 pix.
= 136.96 Å

Surface

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Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.584693 - 1.6222057
Average (Standard dev.)-0.00031995162 (±0.051120296)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 136.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73305_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_73305_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of 1/2 DS DNA, EBNA1 DBD (401-607), TRF2, and Rap1

EntireName: Complex of 1/2 DS DNA, EBNA1 DBD (401-607), TRF2, and Rap1
Components
  • Complex: Complex of 1/2 DS DNA, EBNA1 DBD (401-607), TRF2, and Rap1

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Supramolecule #1: Complex of 1/2 DS DNA, EBNA1 DBD (401-607), TRF2, and Rap1

SupramoleculeName: Complex of 1/2 DS DNA, EBNA1 DBD (401-607), TRF2, and Rap1
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 300 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
10.0 mMHEPES
30.0 mMPotassium Chloride
5.0 mMMagnesium Chloride
1.0 mMZinc Chloride
5.0 mMbeta-mercaptoethanol
0.004 %NP-40
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.03 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7u1t


Details: Cryo-EM structure of 1/2 DS with EBNA1 DBD (PDB 7U1T) was used as a starting point for this map, which includes the 1/2 DS and EBNA1 DBD along with TRF2 and Rap1.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 40377
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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