6NPI | pdb_00006npi

Crystal structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, bound to fragments

• PDB DOI: https://doi.org/10.2210/pdb6NPI/pdb

• Classification: viral protein/inhibitor
• Organism(s): Human herpesvirus 4 strain B95-8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-17 Released: 2019-03-20 
• Deposition Author(s): Messick, T.E.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.163 (Depositor), 0.162 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.142 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

Literature

Structure-based design of small-molecule inhibitors of EBNA1 DNA binding blocks Epstein-Barr virus latent infection and tumor growth.

Messick, T.E., Smith, G.R., Soldan, S.S., McDonnell, M.E., Deakyne, J.S., Malecka, K.A., Tolvinski, L., van den Heuvel, A.P.J., Gu, B.W., Cassel, J.A., Tran, D.H., Wassermann, B.R., Zhang, Y., Velvadapu, V., Zartler, E.R., Busson, P., Reitz, A.B., Lieberman, P.M.

(2019) Sci Transl Med 11

• PubMed: 30842315 
• DOI: https://doi.org/10.1126/scitranslmed.aau5612
• Primary Citation Related Structures: 
  6NPI, 6NPM, 6NPP


• PubMed Abstract: 
  

  Epstein-Barr virus (EBV) is a DNA tumor virus responsible for 1 to 2% of human cancers including subtypes of Burkitt's lymphoma, Hodgkin's lymphoma, gastric carcinoma, and nasopharyngeal carcinoma (NPC). Persistent latent infection drives EBV-associated tumorigenesis. Epstein-Barr nuclear antigen 1 (EBNA1) is the only viral protein consistently expressed in all EBV-associated tumors and is therefore an attractive target for therapeutic intervention. It is a multifunctional DNA binding protein critical for viral replication, genome maintenance, viral gene expression, and host cell survival. Using a fragment-based approach and x-ray crystallography, we identify a 2,3-disubstituted benzoic acid series that selectively inhibits the DNA binding activity of EBNA1. We characterize these inhibitors biochemically and in cell-based assays, including chromatin immunoprecipitation and DNA replication assays. In addition, we demonstrate the potency of EBNA1 inhibitors to suppress tumor growth in several EBV-dependent xenograft models, including patient-derived xenografts for NPC. These inhibitors selectively block EBV gene transcription and alter the cellular transforming growth factor-β (TGF-β) signaling pathway in NPC tumor xenografts. These EBNA1-specific inhibitors show favorable pharmacological properties and have the potential to be further developed for the treatment of EBV-associated malignancies.

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Organizational Affiliation: 
• The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA. [e-mail] [e-mail].
Fox Chase Chemical Diversity Center Inc., 3805 Old Easton Road, Doylestown, PA 18902, USA.
The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA.
Vironika LLC, 3624 Market Street, Ste 5E, Philadelphia, PA 19104, USA.
Quantum Tessera Consulting LLC, 508 Tawnyberry Lane, Collegeville, PA 19426, USA.
Institut Gustave Roussy, 114 Rue Edouard Vaillant, 84800 Villejuif, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 31.11 kDa 
• Atom Count: 2,623 
• Modeled Residue Count: 274 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epstein-Barr nuclear antigen 1	A, B	141	Human herpesvirus 4 strain B95-8	Mutation(s): 0  Gene Names: EBNA1, BKRF1 EC: 3.1.21
UniProt
Find proteins for P03211 (Epstein-Barr virus (strain B95-8)) Explore P03211  Go to UniProtKB:  P03211

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KW1	D [auth B]	({2-[(4-bromo-5-methyl-1,2-oxazol-3-yl)amino]-2-oxoethyl}sulfanyl)acetic acid C8 H9 Br N2 O4 S CMJFFJICEDWDAG-UHFFFAOYSA-N
60Q	C [auth B]	2-pyrrol-1-ylbenzoic acid C11 H9 N O2 GNWTWXOZRSBCOZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.163 (Depositor), 0.162 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.142 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.704	α = 90
b = 67.452	β = 90
c = 69.498	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): Messick, T.E.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	WT096496

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description