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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SV40 LARGE T-ANTIGEN ORIGIN BINING DOMAIN BOUND TO SITE I DNA
 
Authors :  G. Meinke, A. Bohm, P. A. Bullock
Date :  04 Jun 12  (Deposition) - 23 Jan 13  (Release) - 27 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,Y,Z
Keywords :  Origin Binding Domain, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Meinke, P. J. Phelan, C. J. Harrison, P. A. Bullock
Analysis Of The Costructure Of The Simian Virus 40 T-Antige Origin Binding Domain With Site I Reveals A Correlation Between Gaggc Spacing And Spiral Assembly.
J. Virol. V. 87 2923 2013
PubMed-ID: 23269808  |  Reference-DOI: 10.1128/JVI.02549-12

(-) Compounds

Molecule 1 - LARGE T ANTIGEN
    Chains: A, B
    EC Number: 3.6.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Fragment: ORIGIN BINDING DOMAIN, UNP RESIDUES 131-260
    Organism Common: SV40
    Organism Scientific: SIMIAN VIRUS 40
    Organism Taxid: 10633
    Synonym: LT, LT-AG
 
Molecule 2 - SITE I DNA
    Chains: Z
    Engineered: YES
    Organism Scientific: SIMIAN VIRUS 40
    Organism Taxid: 10633
    Other Details: THIS DNA SEQUENCE IS TERMED SITE 1 IN SV40
    Synthetic: YES
 
Molecule 3 - SITE I DNA
    Chains: Y
    Engineered: YES
    Organism Scientific: SIMIAN VIRUS 40
    Organism Taxid: 10633
    Other Details: THIS DNA SEQUENCE IS FROM SV40 SITE I
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABYZ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4FGN)

(-) Sites  (0, 0)

(no "Site" information available for 4FGN)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FGN)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:239 -Pro A:240
2Asp B:239 -Pro B:240

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FGN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FGN)

(-) Exons   (0, 0)

(no "Exon" information available for 4FGN)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhh.........eeeeeeeehhhhhhhhhhhhhhhh...eeeeee....eeeeeeeeeeehhhhhhhhhhh......eeeee..hhhhhhhhhhh....eeee...hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4fgn A 133 EDPKDFPSELLSFLSHAVFSNRTLACFAIYTTKEKAALLYKKIMEKYSVTFISRHNSYNHNILFFLTPHRHRVSAINNYAQKLCTFSFLICKGVNKEYLMYSALTRDPFSVIEESLPGGLKEHDFN 258
                                   142       152       162       172       182       192       202       212       222       232       242       252      


Chain B from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh.........eeeeeeee....hhhhhhhhhhhhh..eeeeee....eeeeeeeeeeehhhhhhhhhhhhh...........hhhhhhhhhhh...eeeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fgn B 134 DPKDFPSELLSFLSHAVFSNRTLACFAIYTTKEKAALLYKKIMEKYSVTFISRHNSYNHNILFFLTPHRHRVSAINNYAQKLCTFSFLICKGVNKEYLMYSALTRDPFSVIEESLPGGLKEHDF 257
                                   143       153       163       173       183       193       203       213       223       233       243       253    


Chain Y from PDB  Type:DNA  Length:23
                                                       
                 4fgn Y   1 GAGGAGGCTTTTTTGGAGGCCTT  23
                                    10        20   


Chain Z from PDB  Type:DNA  Length:23
                                                       
                 4fgn Z   1 AGGCCTCCAAAAAAGCCTCCTCA  23
                                    10        20
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4FGN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FGN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FGN)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)

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  Sites
(no "Sites" information available for 4fgn)
 
  Cis Peptide Bonds
    Asp A:239 - Pro A:240   [ RasMol ]  
    Asp B:239 - Pro B:240   [ RasMol ]  
 

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  3.6.4.-
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LT_SV40 | P03070: 1ejl 1gh6 1n25 1q1s 1q1t 1svl 1svm 1svo 1tbd 1z1d 2fuf 2h1l 2if9 2ipr 2itj 2itl 2nl8 2ntc 2tbd 3qk2 3qn2 4e2i 4gdf 4rxh 5d9i 5tct

(-) Related Entries Specified in the PDB File

2fuf APO-LARGE T-ANTIGEN ORIGIN BINDING DOMAIN
2itl LARGE T-ANTIGEN ORIGIN BINDING DOMAIN IN COMPLEX WITH SITE II DNA (P1-P4)
2ntc LARGE T-ANTIGEN ORIGIN BINDING DOMAIN IN COMPLEX WITH SUBSET OF SITE II DNA (P1, P3)