PDBsum entry: 1b3t

Protein/DNA

PDB id: 1b3t

Contents

Protein chains

147 a.a. *

DNA/RNA

Waters ×182

* Residue conservation analysis

PDB id:

1b3t

Name:

Protein/DNA

Title:

Ebna-1 nuclear protein/DNA complex

Structure:

DNA (5'- d( Gp Gp Gp Ap Ap Gp Cp Ap Tp Ap Tp Gp Cp Tp Tp Cp Cp C)- 3'). Chain: c, d. Engineered: yes. Protein (nuclear protein ebna1). Chain: a, b. Fragment: DNA-binding and dimerization domain residues 459 - 607.

Source:

Synthetic: yes. Human herpesvirus 4. Epstein-barr virus. Organism_taxid: 10376. Strain: gd1. Cellular_location: nuclear. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.20Å R-factor: 0.208 R-free: 0.268

Authors:

A.Bochkarev,E.Bochkareva,A.Edwards,L.Frappier

Key ref:

A.Bochkarev et al. (1998). The 2.2 A structure of a permanganate-sensitive DNA site bound by the Epstein-Barr virus origin binding protein, EBNA1. J Mol Biol, 284, 1273-1278. PubMed id: 9878348 DOI: 10.1006/jmbi.1998.2247

Date:

14-Dec-98 Release date: 15-Dec-98

Protein chains

P03211  (EBNA1_EBVB9) -  Epstein-Barr nuclear antigen 1

Seq: 641 a.a.

Struc: 147 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: host cell nucleus (1 term)
• Biological process: regulation of DNA replication (4 terms)
• Biochemical function: DNA binding (3 terms)

DOI no: 10.1006/jmbi.1998.2247

J Mol Biol 284:1273-1278 (1998)

PubMed id: 9878348

The 2.2 A structure of a permanganate-sensitive DNA site bound by the Epstein-Barr virus origin binding protein, EBNA1.

A.Bochkarev, E.Bochkareva, L.Frappier, A.M.Edwards.

ABSTRACT

Epstein-Barr nuclear antigen 1 (EBNA1) binds to four recognition sites in the minimal origin of latent DNA replication of Epstein-Barr virus and activates latent-phase replication of the viral genomes. Two of these EBNA1 binding sites become sensitive to permanganate oxidation when bound by the DNA binding and dimerization domains of EBNA1. We have previously solved the co-crystal structure of this EBNA1 fragment bound to a consensus recognition site that is not sensitive to permanganate oxidation (CS). To understand the structural difference that underlies the permanganate sensitivity of EBNA1 binding sites, we have now solved the crystal structure of the EBNA1 DNA-binding and dimerization domains bound to a permanganate-sensitive site (CSA/T). Comparisons of permanganate-sensitive and insensitive EBNA1-DNA complexes have revealed only minor differences in protein and DNA structures. In the EBNA1-CSA/T structure, interstrand H-bonds for three consecutive base-pairs centered over the permanganate-sensitive thymine base are lengthened relative to the corresponding bonds in the EBNA1-CS complex, and three potential intrastrand H-bonds were observed between adjacent bases. We also observed that both the CS and CSA/T sequences are overwound by EBNA1 in the vicinity of the permanganate-sensitive thymine base. Finally, we show that the permanganate-sensitive thymine base in the CSA/T-EBNA1 complex is more accessible to solvent than the corresponding T in the EBNA-CS complex.

Selected figure(s)

Figure 1.
Figure 1. A dimer of EBNA459-607 bound to the CSA/T DNA. EBNA1 protein (pink) is shown as a rib- bon. The DNA is shown as a stick model with the A delta T base-pair at position 6/-6 coloured in red, the region of the DNA that is most altered in structure relative to B-form DNA coloured in blue, and the remainder of the DNA shown in black. The Figure was generated using Ribbons 2.0 (Carson, 1991).

Figure 3.
Figure 3. Solvent-accessible surface models of EBNA1- DNA complexes. The EBNA1-CSA/T complex showing the accessible surface of the permanganate-sensitive T at position 6 (a) and the T at position 5 (b) in red; (c) the EBNA1-CS complex showing the accessible surface of the T at position -6 in red. In all three models, EBNA1 is coloured in blue and the DNA in white. In all cases the T in one half of the palindrome only is visible; the corresponding T in the other half of the palindrome is behind the protein.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 284, 1273-1278) copyright 1998.

Figures were selected by the author.