2NL8

The origin binding domain of the SV40 large T antigen bound non specifically to a 17 bp palindrome DNA (sites 1 and 3)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    2IPR, 2ITJ, 2ITL, 2NL8

  • 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 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 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: 2
MoleculeChainsSequence LengthOrganismDetailsImage
large T antigenB [auth A]133Betapolyomavirus macacaeMutation(s): 1 
Gene Names: large T antigen
UniProt
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
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
18-nt PEN element of the SV40 DNA originA [auth W]18N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.87α = 90
b = 43.87β = 90
c = 238.308γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: 2021-10-20
    Changes: Database references