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 
  • R-Value Observed: 0.204 

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:  
    2NL8, 2IPR, 2ITL, 2ITJ

  • 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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
large T antigenAB133Macaca mulatta polyomavirus 1Mutation(s): 0 
Gene Names: large T antigen
Find proteins for Q98ZP7 (Simian virus 40)
Explore Q98ZP7 
Go to UniProtKB:  Q98ZP7
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
24-nt PEN element of the SV40 DNA originW24N/A
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
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 
  • R-Value Observed: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.196α = 90
b = 64.096β = 120.69
c = 79.177γ = 90
Software Package:
Software NamePurpose
CHESSdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-12
    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: 2018-01-24
    Changes: Structure summary