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(-) Description

Title :  CRYSTAL STRUCTURE OF THE JCV LARGE T-ANTIGEN ORIGIN BINDING DOMAIN
 
Authors :  G. Meinke, A. Bohm, P. Bullock
Date :  10 Jul 13  (Deposition) - 02 Apr 14  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Origin Binding Domain, Dna Replication, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Meinke, P. J. Phelan, R. Kalekar, J. Shin, J. Archambault, A. Bohm, P. A. Bullock
Insights Into The Initiation Of Jc Virus Dna Replication Derived From The Crystal Structure Of The T-Antigen Origin Binding Domain.
Plos Pathog. V. 10 03966 2014
PubMed-ID: 24586168  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1003966

(-) Compounds

Molecule 1 - LARGE T ANTIGEN
    Chains: A, B
    EC Number: 3.6.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ORIGIN BINDING DOMAIN (UNP RESIDUES 132-261)
    Gene: LARGE T ANTIGEN
    Organism Common: JCPYV
    Organism Scientific: JC POLYOMAVIRUS
    Organism Taxid: 10632
    Synonym: LT, LT-AG

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1FLC2Ligand/IonCITRATE ANION
2GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FLC-1Ligand/IonCITRATE ANION
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1FLC2Ligand/IonCITRATE ANION
2GOL1Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:249 , ASP A:257 , HOH A:440 , HOH A:499 , HOH A:573BINDING SITE FOR RESIDUE GOL A 301
2AC2SOFTWAREHIS A:204 , ALA A:208 , HIS B:202 , ARG B:203 , HOH B:417 , HOH B:441 , HOH B:447 , HOH B:452 , HOH B:475 , HOH B:476 , HOH B:567 , HOH B:574BINDING SITE FOR RESIDUE FLC B 301
3AC3SOFTWAREASN A:228 , LYS A:229 , GLU A:230 , ASN A:259 , GLU A:261 , SER B:153 , ASN B:154 , HOH B:478 , HOH B:489 , HOH B:542 , HOH B:576BINDING SITE FOR RESIDUE FLC B 302
4AC4SOFTWAREASN A:259 , SER B:148 , ALA B:150 , SER B:153 , ARG B:155 , VAL B:206 , GLY B:226 , HOH B:428 , HOH B:486BINDING SITE FOR RESIDUE GOL B 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Thr A:218 -Phe A:219
2Gln A:240 -Pro A:241
3Gln B:240 -Pro B:241

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LMD)

(-) Sequences/Alignments

Asymmetric 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    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
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:128
                                                                                                                                                                
               SCOP domains d4lmda_ A: The origin DNA-binding domain of SV40 T-antigen                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhh.........eeeeeeeeehhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeeeeehhhhhhhhhhhh.....eeeee..hhhhhhhhh.....eeeee......hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lmd A 134 EDPKDFPVDLHAFLSQAVFSNRTVASFAVYTTKEKAQILYKKLMEKYSVTFISRHGFGGHNILFFLTPHRHRVSAINNYCQKLCTFSFLICKGVNKEYLFYSALCRQPYAVVEESIQGGLKEHDFNPE 261
                                   143       153       163       173       183       193       203       213       223       233       243       253        


Chain B from PDB  Type:PROTEIN  Length:130
                                                                                                                                                                  
               SCOP domains d4lmdb_ B: The origin DNA-binding domain of SV40 T-antigen                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhh.........eeeeeeeeehhhhhhhhhhhhhhhh..eeeeeee..eeeeeeeeeeeehhhhhhhhhhhhhh....eeee..hhhhhhhhh.....eeeee......hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lmd B 132 KVEDPKDFPVDLHAFLSQAVFSNRTVASFAVYTTKEKAQILYKKLMEKYSVTFISRHGFGGHNILFFLTPHRHRVSAINNYCQKLCTFSFLICKGVNKEYLFYSALCRQPYAVVEESIQGGLKEHDFNPE 261
                                   141       151       161       171       181       191       201       211       221       231       241       251       261
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        LT_POVJC | P03072: 4lif 4nbp 5cyn 5j40 5j47 5j4v 5j4y

(-) Related Entries Specified in the PDB File

4lif 4lmd