Crystal Structure of SV40 T-antigen origin binding domain disulfide-linked dimer

Experimental Data Snapshot

  • Resolution: 2.59 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.208 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1371/journal.pbio.0050023
  • Primary Citation of Related Structures:  
    2IF9, 2NTC

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Large T antigen
A, B
134Betapolyomavirus macacaeMutation(s): 0 
Gene Names: large T-antigen
Find proteins for Q98ZP7 (Simian virus 40)
Explore Q98ZP7 
Go to UniProtKB:  Q98ZP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ98ZP7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.59 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.463α = 90
b = 63.982β = 94.45
c = 63.228γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Refinement description