2ITL

The origin binding domain of the SV40 large T antigen bound to the functional pen palindrome DNA (23 bp)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA

Bochkareva, E.Martynowski, D.Seitova, A.Bochkarev, A.

(2006) Embo J. 25: 5961-5969

  • DOI: 10.1038/sj.emboj.7601452
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori) in simian virus 40 (SV40). Here, we determined the crystal structures of the T-ag origin-binding domain (OBD) in apo form, and bound to ...

    The large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori) in simian virus 40 (SV40). Here, we determined the crystal structures of the T-ag origin-binding domain (OBD) in apo form, and bound to either a 17 bp palindrome (sites 1 and 3) or a 23 bp ori DNA palindrome comprising all four GAGGC binding sites for OBD. The T-ag OBDs were shown to interact with the DNA through a loop comprising Ser147-Thr155 (A1 loop), a combination of a DNA-binding helix and loop (His203-Asn210), and Asn227. The A1 loop traveled back-and-forth along the major groove and accounted for most of the sequence-determining contacts with the DNA. Unexpectedly, in both T-ag-DNA structures, the T-ag OBDs bound DNA independently and did not make direct protein-protein contacts. The T-ag OBD was also captured bound to a non-consensus site ATGGC even in the presence of its canonical site GAGGC. Our observations taken together with the known biochemical and structural features of the T-ag-origin interaction suggest a model for origin unwinding.


    Organizational Affiliation

    Banting and Best Department of Medical Research & Department of Medical Genetics and Microbiology, University of Toronto, 100 College St., Toronto, Ontario, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
large T antigen
A, B
133Simian virus 40
Find proteins for Q98ZP7 (Simian virus 40)
Go to UniProtKB:  Q98ZP7
Entity ID: 1
MoleculeChainsLengthOrganism
24-nt PEN element of the SV40 DNA originW24N/A
Entity ID: 2
MoleculeChainsLengthOrganism
24-nt PEN element of the SV40 DNA originC24N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 83.196α = 90.00
b = 64.096β = 120.69
c = 79.177γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CHESSdata collection
REFMACrefinement
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description
  • Version 1.4: 2018-01-24
    Type: Structure summary