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(-) Description

Title :  CRYSTAL STRUCTURE OF HPV6A E2 DNA BINDING DOMAIN BOUND TO A 16 BASE PAIR DNA TARGET
 
Authors :  E. Hooley, R. L. Brady, K. Gaston
Date :  07 Sep 05  (Deposition) - 22 Aug 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Dna Complex, Double Helix, Beta Barrel, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Hooley, V. Fairweather, A. R. Clarke, K. Gaston, R. L. Brady
The Recognition Of Local Dna Conformation By The Human Papillomavirus Type 6 E2 Protein.
Nucleic Acids Res. V. 34 3897 2006
PubMed-ID: 16914454  |  Reference-DOI: 10.1093/NAR/GKL466

(-) Compounds

Molecule 1 - 5'-D(*CP*AP*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*TP*TP*G)-3'
    Chains: C, D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - REGULATORY PROTEIN E2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK223-3
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C TERMINAL DOMAIN
    Gene: E2
    Organism Scientific: HUMAN PAPILLOMAVIRUS TYPE 6A
    Organism Taxid: 37122

 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 2AYB)

(-) Sites  (0, 0)

(no "Site" information available for 2AYB)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AYB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2AYB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AYB)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 2AYB)

(-) 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:87
 aligned with VE2_HPV6A | Q84294 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:87
                                   291       301       311       321       331       341       351       361       
           VE2_HPV6A    282 SSATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSLHLL  368
               SCOP domains d2ayba1 A:281-366 Papillomavirus-1 E2 protein                                           SCOP domains
               CATH domains 2aybA00 A:281-366  [code=3.30.70.330, no name defined]                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeehhhhhhhhhhhhhhhhhhhh..................eeeeee..hhhhhhhhhhhh......eeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                2ayb A  281 SSATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSMHLL  366
                                   290       300    |  309       319       329       339       349       359       
                                                 304A                                                              


Chain B from PDB  Type:PROTEIN  Length:87
 aligned with VE2_HPV6A | Q84294 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:87
                                   291       301       311       321       331       341       351       361       
           VE2_HPV6A    282 SSATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSLHLL  368
               SCOP domains d2aybb1 B:281-366 Papillomavirus-1 E2 protein                                           SCOP domains
               CATH domains 2aybB00 B:281-366  [code=3.30.70.330, no name defined]                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeehhhhhhhhhhhhhhhhhhhh..................eeeeee..hhhhhhhhhhhh......eeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                2ayb B  281 SSATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSMHLL  366
                                   290       300    |  309       319       329       339       349       359       
                                                 304A                                                              


Chain C from PDB  Type:DNA  Length:16
                                                 
                2ayb C    1 CAACCGAATTCGGTTG   16
                                    10      


Chain D from PDB  Type:DNA  Length:16
                                                 
                2ayb D    1 CAACCGAATTCGGTTG   16
                                    10
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  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  (0, 0)

(no "Pfam Domain" information available for 2AYB)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (VE2_HPV6A | Q84294)
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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VE2_HPV6A | Q84294: 1r8h 2aye 2ayg

(-) Related Entries Specified in the PDB File

2aye 2ayg