2NTC

Crystal Structure of sv40 large T antigen origin binding domain with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Crystal Structure of the SV40 T-Antigen Origin Binding Domain in Complex with DNA

Meinke, G.Phelan, P.Moine, S.Bochkareva, E.Bochkarev, A.Bullock, P.A.Bohm, A.

(2007) Plos Biol. 5: e23-e23

  • DOI: 10.1371/journal.pbio.0050023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA replication is initiated upon binding of "initiators" to origins of replication. In simian virus 40 (SV40), the core origin contains four pentanucleotide binding sites organized as pairs of inverted repeats. Here we describe the crystal structure ...

    DNA replication is initiated upon binding of "initiators" to origins of replication. In simian virus 40 (SV40), the core origin contains four pentanucleotide binding sites organized as pairs of inverted repeats. Here we describe the crystal structures of the origin binding domain (obd) of the SV40 large T-antigen (T-ag) both with and without a subfragment of origin-containing DNA. In the co-structure, two T-ag obds are oriented in a head-to-head fashion on the same face of the DNA, and each T-ag obd engages the major groove. Although the obds are very close to each other when bound to this DNA target, they do not contact one another. These data provide a high-resolution structural model that explains site-specific binding to the origin and suggests how these interactions help direct the oligomerization events that culminate in assembly of the helicase-active dodecameric complex of T-ag.


    Organizational Affiliation

    Department of Biochemistry, School of Medicine, and the Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
large T antigen
A, B
134Simian virus 40
Find proteins for Q98ZP7 (Simian virus 40)
Go to UniProtKB:  Q98ZP7
Entity ID: 1
MoleculeChainsLengthOrganism
21-nt PEN element of the SV40 DNA originW21N/A
Entity ID: 2
MoleculeChainsLengthOrganism
21-nt PEN element of the SV40 DNA originC21N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.489α = 90.00
b = 68.341β = 90.00
c = 97.262γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance