Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  ASYMMETRIC ASSEMBLY OF MERKEL CELL POLYOMAVIRUS LARGE T-ANTIGEN ORIGIN BINDING DOMAINS AT THE VIRAL ORIGIN
 
Authors :  C. J. Harrison, G. Meinke, A. Bohm
Date :  22 Jan 11  (Deposition) - 27 Apr 11  (Release) - 15 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,E,W
Keywords :  Origin Binding Domain, Protein-Dna Complex, Replication, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Harrison, G. Meinke, H. J. Kwun, H. Rogalin, P. J. Phelan, P. A. Bullock, Y. Chang, P. S. Moore, A. Bohm
Asymmetric Assembly Of Merkel Cell Polyomavirus Large T-Antigen Origin Binding Domains At The Viral Origin.
J. Mol. Biol. V. 409 529 2011
PubMed-ID: 21501625  |  Reference-DOI: 10.1016/J.JMB.2011.03.051

(-) Compounds

Molecule 1 - LARGE T ANTIGEN
    Chains: A, B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ORIGIN BINDING DOMAIN (UNP RESIDUES 308-433)
    Organism Scientific: MERKEL CELL POLYOMAVIRUS
    Organism Taxid: 493803
 
Molecule 2 - DNA (26-MER)
    Chains: W
    Engineered: YES
    Other Details: MERKEL CELL VIRUS ORIGIN SITE 1/2 (WATSON STRAND)
    Other Details - Source: SYNTHESIZED
    Synthetic: YES
 
Molecule 3 - DNA (26-MER)
    Chains: C
    Engineered: YES
    Other Details: MERKEL CELL VIRUS ORIGIN SITE 1/2 (CRICK STRAND)
    Other Details - Source: SYNTHESIZED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCEW

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3QFQ)

(-) Sites  (0, 0)

(no "Site" information available for 3QFQ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QFQ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val B:311 -Pro B:312

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QFQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QFQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3QFQ)

(-) 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    
   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:119
 aligned with E2IPT4_9POLY | E2IPT4 from UniProtKB/TrEMBL  Length:739

    Alignment length:119
                                   240       250       260       270       280       290       300       310       320       330       340         
         E2IPT4_9POLY   231 TPVPTDFPIDLSDYLSHAVYSNKTVSCFAIYTTSDKAIELYDKIEKFKVDFKSRHACELGCILLFITLSKHRVSAIKNFCSTFCTISFLICKGVNKMPEMYNNLCKPPYKLLQENKPLL 349
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh............eeeeee..hhhhhhhhhhhhhhh.eeeeeeee....eeeeeeeeeeehhhhhhhhh..........eee..hhhhhhhhh......eeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3qfq A 309 TPVPTDFPIDLSDYLSHAVYSNKTVSCFAIYTTSDKAIELYDKIEKFKVDFKSRHACELGCILLFITLSKHRVSAIKNFCSTFCTISFLICKGVNKMPEMYNNLCKPPYKLLQENKPLL 427
                                   318       328       338       348       358       368       378       388       398       408       418         


Chain B from PDB  Type:PROTEIN  Length:120
 aligned with E2IPT4_9POLY | E2IPT4 from UniProtKB/TrEMBL  Length:739

    Alignment length:120
                                   240       250       260       270       280       290       300       310       320       330       340       350
         E2IPT4_9POLY   231 TPVPTDFPIDLSDYLSHAVYSNKTVSCFAIYTTSDKAIELYDKIEKFKVDFKSRHACELGCILLFITLSKHRVSAIKNFCSTFCTISFLICKGVNKMPEMYNNLCKPPYKLLQENKPLLN 350
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhh............eeeeeeeehhhhhhhhhhhh....eeeeee......eeeeeeeeeeehhhhhhhhhhhhh.....eeee..hhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qfq B 309 TPVPTDFPIDLSDYLSHAVYSNKTVSCFAIYTTSDKAIELYDKIEKFKVDFKSRHACELGCILLFITLSKHRVSAIKNFCSTFCTISFLICKGVNKMPEMYNNLCKPPYKLLQENKPLLN 428
                                   318       328       338       348       358       368       378       388       398       408       418       428


Chain C from PDB  Type:DNA  Length:26
                                                          
                 3qfq C   1 CGGAGGCTAGGAGCCCCAAGCCTCTG  26
                                    10        20      


Chain E from PDB  Type:PROTEIN  Length:117
 aligned with E2IPT4_9POLY | E2IPT4 from UniProtKB/TrEMBL  Length:739

    Alignment length:117
                                   242       252       262       272       282       292       302       312       322       332       342       
         E2IPT4_9POLY   233 VPTDFPIDLSDYLSHAVYSNKTVSCFAIYTTSDKAIELYDKIEKFKVDFKSRHACELGCILLFITLSKHRVSAIKNFCSTFCTISFLICKGVNKMPEMYNNLCKPPYKLLQENKPLL 349
               SCOP domains d3qfqe_ E: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --T_Ag_DNA_bind-3qfqE01 E:313-405                                                              ---------------------- Pfam domains (1)
           Pfam domains (2) --T_Ag_DNA_bind-3qfqE02 E:313-405                                                              ---------------------- Pfam domains (2)
           Pfam domains (3) --T_Ag_DNA_bind-3qfqE03 E:313-405                                                              ---------------------- Pfam domains (3)
         Sec.struct. author .....hhhhh............eeeeeeeehhhhhhhhhhhhhhh.eeeeeee.....eeeeeeeeeeehhhhhhhhhh........eeee..hhhhhhhhh......eeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3qfq E 311 VPTDFPIDLSDYLSHAVYSNKTVSCFAIYTTSDKAIELYDKIEKFKVDFKSRHACELGCILLFITLSKHRVSAIKNFCSTFCTISFLICKGVNKMPEMYNNLCKPPYKLLQENKPLL 427
                                   320       330       340       350       360       370       380       390       400       410       420       


Chain W from PDB  Type:DNA  Length:26
                                                          
                 3qfq W   1 GCAGAGGCTTGGGGCTCCTAGCCTCC  26
                                    10        20
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QFQ)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: Rep (10)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,E   (E2IPT4_9POLY | E2IPT4)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003688    DNA replication origin binding    Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3qfq)
 
  Sites
(no "Sites" information available for 3qfq)
 
  Cis Peptide Bonds
    Val B:311 - Pro B:312   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3qfq
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  E2IPT4_9POLY | E2IPT4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  E2IPT4_9POLY | E2IPT4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3QFQ)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3QFQ)