PDBsum entry 4gdf

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protein dna_rna metals Protein-protein interface(s) links
Hydrolase/DNA PDB id
Jmol PyMol
Protein chains
497 a.a.
_ZN ×4
Waters ×79
PDB id:
Name: Hydrolase/DNA
Title: A crystal structure of sv40 large t antigen
Structure: Large t antigen. Chain: a, b, e, f. Fragment: unp residues 131-627. Engineered: yes. DNA (32-mer). Chain: c, g. Engineered: yes. DNA (32-mer). Chain: d, h.
Source: Simian virus 40. Sv40. Organism_taxid: 10633. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: nucleic acid synthesis. Other_details: nucleic acid synthesis
2.80Å     R-factor:   0.227     R-free:   0.255
Authors: Y.P.Chang,M.Xu,X.S.Chen
Key ref: Y.P.Chang et al. (2013). Mechanism of origin DNA recognition and assembly of an initiator-helicase complex by SV40 large tumor antigen. Cell Rep, 3, 1117-1127. PubMed id: 23545501 DOI: 10.1016/j.celrep.2013.03.002
31-Jul-12     Release date:   10-Apr-13    
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Protein chains
Pfam   ArchSchema ?
P03070  (LT_SV40) -  Large T antigen
708 a.a.
497 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA replication   1 term 
  Biochemical function     DNA binding     3 terms  


DOI no: 10.1016/j.celrep.2013.03.002 Cell Rep 3:1117-1127 (2013)
PubMed id: 23545501  
Mechanism of origin DNA recognition and assembly of an initiator-helicase complex by SV40 large tumor antigen.
Y.P.Chang, M.Xu, A.C.Machado, X.J.Yu, R.Rohs, X.S.Chen.
The DNA tumor virus Simian virus 40 (SV40) is a model system for studying eukaryotic replication. SV40 large tumor antigen (LTag) is the initiator/helicase that is essential for genome replication. LTag recognizes and assembles at the viral replication origin. We determined the structure of two multidomain LTag subunits bound to origin DNA. The structure reveals that the origin binding domains (OBDs) and Zn and AAA+ domains are involved in origin recognition and assembly. Notably, the OBDs recognize the origin in an unexpected manner. The histidine residues of the AAA+ domains insert into a narrow minor groove region with enhanced negative electrostatic potential. Computational analysis indicates that this region is intrinsically narrow, demonstrating the role of DNA shape readout in origin recognition. Our results provide important insights into the assembly of the LTag initiator/helicase at the replication origin and suggest that histidine contacts with the minor groove serve as a mechanism of DNA shape readout.