7U1T | pdb_00007u1t

EBNA1 DNA binding domain (401-641) binds to half Dyad Symmetry element

• PDB DOI: https://doi.org/10.2210/pdb7U1T/pdb
• NAKB: 7U1T
• EM Map EMD-26305: EMDB EMDataResource

• Classification: VIRAL PROTEIN/DNA
• Organism(s): Human herpesvirus 4 strain B95-8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-02-22 Released: 2023-02-22 
• Deposition Author(s): Mei, Y., Lieberman, P.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

EBNA1 DNA binding domain (401-641) binds to half Dyad Symmetry element

Mei, Y., Lieberman, P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 113.33 kDa 
• Atom Count: 7,574 
• Modeled Residue Count: 793 
• Deposited Residue Count: 830 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epstein-Barr nuclear antigen 1	A, B, C, D	178	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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (59-MER)	E	59	Human herpesvirus 4 strain B95-8

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (59-MER)	F	59	Human herpesvirus 4 strain B95-8

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1.3
MODEL REFINEMENT	PHENIX	1.20
MODEL REFINEMENT	Coot	0.9.6

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-02-22 
Deposition Author(s): Mei, Y., Lieberman, P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	5R01CA093606-18
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)	United States	5R01DE017336-13

Revision History  

• Version 1.0: 2023-02-22
  Type: Initial release
  
• Version 1.1: 2024-06-12
  Changes: Data collection, Refinement description