PDBsum entry 2ntc

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protein dna_rna links
DNA binding protein/DNA PDB id
Jmol PyMol
Protein chains
127 a.a. *
Waters ×77
* Residue conservation analysis
PDB id:
Name: DNA binding protein/DNA
Title: Crystal structure of sv40 large t antigen origin binding dom DNA
Structure: 21-nt pen element of the sv40 DNA origin. Chain: w. Engineered: yes. 21-nt pen element of the sv40 DNA origin. Chain: c. Engineered: yes. Large t antigen. Chain: a, b. Fragment: origin binding domain (residues 131-259).
Source: Synthetic: yes. Simian virus 40. Organism_taxid: 10633. Strain: 776. Gene: large t antigen. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
2.40Å     R-factor:   0.209     R-free:   0.287
Authors: A.Bohm,G.Meinke,P.A.Bullock
Key ref: G.Meinke et al. (2007). The crystal structure of the SV40 T-antigen origin binding domain in complex with DNA. PLoS Biol, 5, e23. PubMed id: 17253903
07-Nov-06     Release date:   13-Feb-07    
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Protein chains
Pfam   ArchSchema ?
Q98ZP7  (Q98ZP7_SV40) -  Truncated large tumor antigen
537 a.a.
127 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA replication   1 term 
  Biochemical function     DNA replication origin binding     1 term  


PLoS Biol 5:e23 (2007)
PubMed id: 17253903  
The crystal structure of the SV40 T-antigen origin binding domain in complex with DNA.
G.Meinke, P.Phelan, S.Moine, E.Bochkareva, A.Bochkarev, P.A.Bullock, A.Bohm.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21636896 G.Meinke, P.Phelan, A.Fradet-Turcotte, J.Archambault, and P.A.Bullock (2011).
Structure-based design of a disulfide-linked oligomeric form of the simian virus 40 (SV40) large T antigen DNA-binding domain.
  Acta Crystallogr D Biol Crystallogr, 67, 560-567.
PDB code: 3qn2
20219473 I.Cuesta, R.Núñez-Ramírez, S.H.Scheres, D.Gai, X.S.Chen, E.Fanning, and J.M.Carazo (2010).
Conformational rearrangements of SV40 large T antigen during early replication events.
  J Mol Biol, 397, 1276-1286.  
19625393 A.Hermannstädter, C.Ziegler, M.Kühl, W.Deppert, and G.V.Tolstonog (2009).
Wild-type p53 enhances efficiency of simian virus 40 large-T-antigen-induced cellular transformation.
  J Virol, 83, 10106-10118.  
19101707 E.Fanning, and K.Zhao (2009).
SV40 DNA replication: from the A gene to a nanomachine.
  Virology, 384, 352-359.  
19759150 H.J.Kwun, A.Guastafierro, M.Shuda, G.Meinke, A.Bohm, P.S.Moore, and Y.Chang (2009).
The minimum replication origin of merkel cell polyomavirus has a unique large T-antigen loading architecture and requires small T-antigen expression for optimal replication.
  J Virol, 83, 12118-12128.  
19946136 M.L.Bochman, and A.Schwacha (2009).
The Mcm complex: unwinding the mechanism of a replicative helicase.
  Microbiol Mol Biol Rev, 73, 652-683.  
18579587 A.Kumar, W.S.Joo, G.Meinke, S.Moine, E.N.Naumova, and P.A.Bullock (2008).
Evidence for a structural relationship between BRCT domains and the helicase domains of the replication initiators encoded by the Polyomaviridae and Papillomaviridae families of DNA tumor viruses.
  J Virol, 82, 8849-8862.  
18003733 S.Khopde, and D.T.Simmons (2008).
Simian virus 40 DNA replication is dependent on an interaction between topoisomerase I and the C-terminal end of T antigen.
  J Virol, 82, 1136-1145.  
17596312 A.Fradet-Turcotte, C.Vincent, S.Joubert, P.A.Bullock, and J.Archambault (2007).
Quantitative analysis of the binding of simian virus 40 large T antigen to DNA.
  J Virol, 81, 9162-9174.  
17287270 A.Kumar, G.Meinke, D.K.Reese, S.Moine, P.J.Phelan, A.Fradet-Turcotte, J.Archambault, A.Bohm, and P.A.Bullock (2007).
Model for T-antigen-dependent melting of the simian virus 40 core origin based on studies of the interaction of the beta-hairpin with DNA.
  J Virol, 81, 4808-4818.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.