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(-) Description

Title :  MODEL FOR BINDING OF E2F8 DBDS TO E2F CONSENSUS SEQUENCE BASED UPON STRUCTURAL HOMOLOGY TO E2F4/DP2
 
Authors :  B. Maiti, J. Li, A. De Bruin, F. Gordon, C. Timmers, R. Opavsky, K. Patil, J. Tuttle, W. Cleghorn, G. Leone
Date :  05 Mar 05  (Deposition) - 29 Mar 05  (Release) - 21 Jun 05  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,D,E,F
Keywords :  Winged Helix-Turn-Helix, Dna Binding Domains (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Maiti, J. Li, A. De Bruin, F. Gordon, C. Timmers, R. Opavsky, K. Patil, J. Tuttle, W. Cleghorn, G. Leone
Cloning And Characterization Of Mouse E2F8, A Novel Mammalian E2F Family Member Capable Of Blocking Cellular Proliferation
J. Biol. Chem. V. 280 18211 2005
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIKEN CDNA 4432406C08
    ChainsA
    FragmentDNA BINDING DOMAIN TWO
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    SynonymE2F8 DBD2
 
Molecule 2 - 5'- D(P*TP*TP*TP*TP*CP*GP*CP*GP*CP*GP*GP*TP*TP*TP*T)-3'
    ChainsD
 
Molecule 3 - 5'- D(P*AP*AP*AP*AP*CP*CP*GP*CP*GP*CP*GP*AP*AP*AP*A)-3'
    ChainsE
 
Molecule 4 - RIKEN CDNA 4432406C08
    ChainsF
    FragmentDNA BINDING DOMAIN ONE
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    SynonymE2F8 DBD1

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1WZH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WZH)

(-) Sequences/Alignments

Theoretical Model
   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:79
 aligned with E2F8_MOUSE | Q58FA4 from UniProtKB/Swiss-Prot  Length:860

    Alignment length:79
                                   272       282       292       302       312       322       332         
           E2F8_MOUSE   263 DKSLRVMSQKFVMLFLVSTPQIVSLEIAAKILIGEDHVEDLDKSKYKTKIRRLYDIANVLSSLDLIKKVHVTEERGRKP 341
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.........ee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 1wzh A 263 DKSLRVMSQKFVMLFLVSTPQIVSLEIAAKILIGEDHVEDLDKSKYKTKIRRLYDIANVLSSLDLIKKVHVTEERGRKP 341
                                   272       282       292       302       312       322       332         

Chain D from PDB  Type:DNA  Length:15
                                               
                 1wzh D 501 TTTTCGCGCGGTTTT 515
                                   510     

Chain E from PDB  Type:DNA  Length:15
                                               
                 1wzh E 601 AAAACCGCGCGAAAA 615
                                   610     

Chain F from PDB  Type:PROTEIN  Length:70
 aligned with E2F8_MOUSE | Q58FA4 from UniProtKB/Swiss-Prot  Length:860

    Alignment length:70
                                   121       131       141       151       161       171       181
           E2F8_MOUSE   112 SRKEKSLGLLCHKFLARYPKYPNPAVNNDICLDEVAEELNVERRRIYDIVNVLESLHMVSRLAKNRYTWH 181
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh...ee.....hhhhhhhh..hhhhhhhhhhhhhhhh.eeeee..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 1wzh F 112 SRKEKSLGLLCHKFLARYPKYPNPAVNNDICLDEVAEELNVERRRIYDIVNVLESLHMVSRLAKNRYTWH 181
                                   121       131       141       151       161       171       181

   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  (0, 0)

(no "SCOP Domain" information available for 1WZH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WZH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WZH)

(-) Gene Ontology  (24, 24)

Theoretical Model(hide GO term definitions)
Chain A,F   (E2F8_MOUSE | Q58FA4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0001047    core promoter binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    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.
    GO:0001078    transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0033301    cell cycle comprising mitosis without cytokinesis    A mitotic cell cycle in which mitosis is completed but cytokinesis does not occur, resulting in a cell containing multiple nuclei each with a chromosomal complement of the original ploidy (usually 2N).
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0060718    chorionic trophoblast cell differentiation    The process in which relatively unspecialized cells of the ectoplacental cone acquire specialized structural and/or functional features that characterize chorionic trophoblasts. These cells will migrate towards the spongiotrophoblast layer and give rise to syncytiotrophoblasts of the labyrinthine layer.
    GO:0070365    hepatocyte differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a hepatocyte. A hepatocyte is specialized epithelial cell that is organized into interconnected plates called lobules, and is the main structural component of the liver.
    GO:0032466    negative regulation of cytokinesis    Any process that stops, prevents, or reduces the frequency, rate or extent of the division of the cytoplasm of a cell, and its separation into two daughter cells.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0001890    placenta development    The process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    GO:0032877    positive regulation of DNA endoreduplication    Any process that activates or increases the frequency, rate or extent of DNA endoreduplication.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0002040    sprouting angiogenesis    The extension of new blood vessels from existing capillaries into avascular tissues resulting from the proliferation of blood vessel endothelial cells.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0060707    trophoblast giant cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a trophoblast giant cell of the placenta. Trophoblast giant cells are the cell of the placenta that line the maternal decidua.
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

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(-) Related Entries Specified in the PDB File

1cf7 THE COORDINATES FOR DNA WERE TAKEN FROM 1CF7