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(-) Description

Title :  HUMAN PAPILLOMAVIRUS TYPE 18 E2 DNA-BINDING DOMAIN BOUND TO ITS DNA TARGET
 
Authors :  S. -S. Kim, J. K. Tam, A. F. Wang, R. S. Hegde
Date :  03 Jul 01  (Deposition) - 13 Jul 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hpv-18, E2, Dna-Binding Domain, E2-Dna Complex, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. S. Kim, J. K. Tam, A. F. Wang, R. S. Hegde
The Structural Basis Of Dna Target Discrimination By Papillomavirus E2 Proteins.
J. Biol. Chem. V. 275 31245 2000
PubMed-ID: 10906136  |  Reference-DOI: 10.1074/JBC.M004541200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - E2 BINDING SITE DNA
    Chains: C, D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - REGULATORY PROTEIN E2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: DNA-BINDING DOMAIN
    Gene: E2
    Organism Scientific: HUMAN PAPILLOMAVIRUS TYPE 18
    Organism Taxid: 333761

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1JJ4)

(-) Sites  (0, 0)

(no "Site" information available for 1JJ4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JJ4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JJ4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JJ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JJ4)

(-) Exons   (0, 0)

(no "Exon" information available for 1JJ4)

(-) 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:74
 aligned with VE2_HPV18 | P06790 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:79
                                   295       305       315       325       335       345       355         
            VE2_HPV18   286 TTPIIHLKGDRNSLKCLRYRLRKHSDHYRDISSTWHWTGAGNEKTGILTVTYHSETQRTKFLNTVAIPDSVQILVGYMT 364
               SCOP domains d1jj4a_ A: Papillomavirus-1 E2 protein                                          SCOP domains
               CATH domains 1jj4A00 A:286-364  [code=3.30.70.330,      no name defined]                     CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeehhhhhhhhhhhhhhhhhh.ee.......-----.eeeeeee..hhhhhhhhhh........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 1jj4 A 286 MTPIIHLKGDRNSLKCLRYRLRKHSDHYRDISSTWHWT-----KTGILTVTYHSETQRTKFLNTVAIPDSVQILVGYMT 364
                                   295       305       315       | -   |   335       345       355         
                                                               323   329                                   


Chain B from PDB  Type:PROTEIN  Length:76
 aligned with VE2_HPV18 | P06790 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:80
                                   294       304       314       324       334       344       354       364
            VE2_HPV18   285 NTTPIIHLKGDRNSLKCLRYRLRKHSDHYRDISSTWHWTGAGNEKTGILTVTYHSETQRTKFLNTVAIPDSVQILVGYMT 364
               SCOP domains d1jj4b_ B: Papillomavirus-1 E2 protein                                           SCOP domains
               CATH domains 1jj4B00 B:285-364  [code=3.30.70.330, n    o name defined]                       CATH domains
           Pfam domains (1) ---PPV_E2_C-1jj4B01 B:288-364                                                    Pfam domains (1)
           Pfam domains (2) ---PPV_E2_C-1jj4B02 B:288-364                                                    Pfam domains (2)
         Sec.struct. author ..eeeeeeeehhhhhhhhhhhhhhhhhhh.ee.......----...eeeeee..hhhhhhhhhhhh......eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                 1jj4 B 285 HMTPIIHLKGDRNSLKCLRYRLRKHSDHYRDISSTWHWT----EKTGILTVTYHSETQRTKFLNTVAIPDSVQILVGYMT 364
                                   294       304       314        |-   |   334       344       354       364
                                                                323  328                                    


Chain C from PDB  Type:DNA  Length:16
                                                
                 1jj4 C 602 CAACCGAATTCGGTTG 617
                                   611      


Chain D from PDB  Type:DNA  Length:16
                                                
                 1jj4 D 902 CAACCGAATTCGGTTG 917
                                   911
   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, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: PPV_E2_C] (7)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (VE2_HPV18 | P06790)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
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.
    GO:0006275    regulation of DNA replication    Any process that modulates the frequency, rate or extent of DNA replication.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0044163    host cytoskeleton    Any of the various filamentous elements that form the internal framework of host cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the host cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the host cell. The various elements of the host cytoskeleton not only serve in the maintenance of host cellular shape but also have roles in other host cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VE2_HPV18 | P06790: 1f9f 1qqh 1tue

(-) Related Entries Specified in the PDB File

1by9 E2 DNA-BINDING DOMAIN FROM HUMAN PAPILLOMAVIRUS TYPE 16
1f9f CRYSTAL STRUCTURE OF THE HPV-18 E2 DNA-BINDING DOMAIN
2bop BOVINE PAPILLOMAVIRUS-1 E2 DNA BINDING DOMAIN BOUND TO ITS DNA TARGET