› 5t7x

X-ray diffraction
2.35Å resolution

Crystal structure of HHV-4 EBNA1 DNA binding domain (patient-derived, nasopharyngeal carcinoma) bound to DNA

Released:
DOI: 10.2210/pdb5t7x/pdb
PDB entry 5t7x coloured by chain, front view.
PDB entry 5t7x coloured by chain, side view.
PDB entry 5t7x coloured by chain, top view.
Source organism: Human herpesvirus 4 strain B95-8
Primary publication:
Carcinoma-risk variant of EBNA1 deregulates Epstein-Barr Virus episomal latency.
Dheekollu J, Malecka K, Wiedmer A, Delecluse HJ, Chiang AK, Altieri DC, Messick TE, Lieberman PM
Oncotarget 8 7248-7264 (2017)
PMID: 28077791

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119142 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Epstein-Barr nuclear antigen 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 149 amino acids
Theoretical weight: 16.33 KDa
Source organism: Human herpesvirus 4 strain B95-8
Expression system: Escherichia coli
UniProt:
  • Canonical: P03211 (Residues: 459-607; Coverage: 23%)
Gene names: BKRF1, EBNA1
Sequence domains: Epstein Barr virus nuclear antigen-1, DNA-binding domain
Structure domains: Epstein Barr virus nuclear antigen-1, DNA-binding domain
DNA (5'-D(*GP*GP*AP*TP*AP*GP*CP*CP*TP*AP*TP*GP*CP*TP*AP*CP*CP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 18 nucleotides
Theoretical weight: 5.48 KDa
Source organism: Human herpesvirus 4 strain B95-8
Expression system: Not provided
DNA (5'-D(*GP*GP*GP*TP*AP*GP*CP*AP*TP*AP*GP*GP*CP*TP*AP*TP*CP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 18 nucleotides
Theoretical weight: 5.56 KDa
Source organism: Human herpesvirus 4 strain B95-8
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P212121
Unit cell:
a: 60.025Å b: 64.904Å c: 111.783Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.185 0.233
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

13 review citations

Epstein-Barr virus-associated lymphomas.
Shannon-Lowe et al. (2017)
12 more

1 mention without citation

Structural and Biophysical Investigation of the Key Hotspots on the Surface of Epstein-Barr Nuclear Antigen 1 Essential for DNA Recognition and Pathogenesis.
Hashmi et al. (2021)