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(-) Description

Title :  STRUCTURAL BASIS OF DNA RECOGNITION BY THE HETERODIMERIC CELL CYCLE TRANSCRIPTION FACTOR E2F-DP
 
Authors :  N. Zheng, E. Fraenkel, C. O. Pabo, N. P. Pavletich
Date :  24 Mar 99  (Deposition) - 02 Apr 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  E2F, Dp, Winged-Helix, Dna-Binding Domain, Transcription Factor, Cell Cycle, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Zheng, E. Fraenkel, C. O. Pabo, N. P. Pavletich
Structural Basis Of Dna Recognition By The Heterodimeric Cell Cycle Transcription Factor E2F-Dp.
Genes Dev. V. 13 666 1999
PubMed-ID: 10090723
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*AP*TP*TP*TP*TP*CP*GP*CP*GP*CP*GP*GP*TP*TP*TP*T)-3')
    Chains: C
    Engineered: YES
    Fragment: ADENOVIRUS TYPE 5 E2 PROMOTER E2F-BINDING SITE
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*TP*AP*AP*AP*AP*CP*CP*GP*CP*GP*CP*GP*AP*AP*AP*A)-3')
    Chains: D
    Engineered: YES
    Fragment: ADENOVIRUS TYPE 5 E2 PROMOTER E2F-BINDING SITE
    Synthetic: YES
 
Molecule 3 - PROTEIN (TRANSCRIPTION FACTOR E2F-4)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cellular Location: CYTOPLASM
    Expression System Cell Line: BL21(DE3)
    Expression System Plasmid: PGEX-4T3
    Expression System Taxid: 562
    Fragment: DNA-BINDING DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - PROTEIN (TRANSCRIPTION FACTOR DP-2)
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cellular Location: CYTOPLASM
    Expression System Cell Line: BL21(DE3)
    Expression System Plasmid: PGEX-4T3
    Expression System Taxid: 562
    Fragment: DNA-BINDING DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 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 1CF7)

(-) Sites  (0, 0)

(no "Site" information available for 1CF7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CF7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CF7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CF7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1CF7)

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003793781ENSE00001480751chr16:67226068-67226265198E2F4_HUMAN1-45451A:16-4530
1.2ENST000003793782ENSE00001480748chr16:67226664-67226773110E2F4_HUMAN46-82371A:46-8237
1.3ENST000003793783ENSE00001503907chr16:67226912-67227073162E2F4_HUMAN82-136551A:82-821
1.4ENST000003793784ENSE00001503906chr16:67227375-6722741844E2F4_HUMAN136-151160--
1.5ENST000003793785ENSE00001480740chr16:67228301-6722836262E2F4_HUMAN151-171210--
1.6ENST000003793786ENSE00001480738chr16:67228589-67228883295E2F4_HUMAN172-270990--
1.7ENST000003793787ENSE00001480736chr16:67229685-67229909225E2F4_HUMAN270-345760--
1.8ENST000003793788ENSE00001480735chr16:67231502-6723154948E2F4_HUMAN345-361170--
1.9ENST000003793789ENSE00001480734chr16:67231770-6723181445E2F4_HUMAN361-376160--
1.10ENST0000037937810ENSE00001480731chr16:67231911-67232821911E2F4_HUMAN376-413380--

(-) 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:67
 aligned with E2F4_HUMAN | Q16254 from UniProtKB/Swiss-Prot  Length:413

    Alignment length:67
                                    25        35        45        55        65        75       
           E2F4_HUMAN    16 SRHEKSLGLLTTKFVSLLQEAKDGVLDLKLAADTLAVRQKRRIYDITNVLEGIGLIEKKSKNSIQWK  82
               SCOP domains d1cf7a_ A: Cell cycle transcription factor E2F-4                    SCOP domains
               CATH domains 1cf7A00 A:16-82 'winged helix' repressor DNA binding domain         CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh....eeehhhhhhh.....hhhhhhhhhhhhhh..eeeee..eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:16-45        Exon 1.2  PDB: A:46-82 UniProt: 46-82 Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------1 Transcript 1 (2)
                 1cf7 A  16 SRHEKSLGLLTTKFVSLLQEAKDGVLDLKLAADTLAVRQKRRIYDITNVLEGIGLIEKKSKNSIQWK  82
                                    25        35        45        55        65        75       


Chain B from PDB  Type:PROTEIN  Length:82
 aligned with TFDP2_HUMAN | Q14188 from UniProtKB/Swiss-Prot  Length:446

    Alignment length:82
                                   138       148       158       168       178       188       198       208  
          TFDP2_HUMAN   129 GKGLRHFSMKVCEKVQRKGTTSYNEVADELVSEFTNSNNHLAADSAYDQKNIRRRVYDALNVLMAMNIISKEKKEIKWIGLP 210
               SCOP domains d1cf7b_ B: Cell cycle transcription factor DP-2                                    SCOP domains
               CATH domains 1cf7B00 B:68-149 'winged helix' repressor DNA binding domain                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhh.hhhhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 1cf7 B  68 GKGLRHFSMKVCEKVQRKGTTSYNEVADELVSEFTNSNNHLAADSAYDQKNIRRRVYDALNVLMAMNIISKEKKEIKWIGLP 149
                                    77        87        97       107       117       127       137       147  


Chain C from PDB  Type:DNA  Length:15
                                               
                 1cf7 C 501 TTTTCGCGCGGTTTT 515
                                   510     


Chain D from PDB  Type:DNA  Length:15
                                               
                 1cf7 D 601 AAAACCGCGCGAAAA 615
                                   610
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CF7)

(-) Gene Ontology  (35, 49)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (E2F4_HUMAN | Q16254)
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:1990841    promoter-specific chromatin binding    Interacting selectively and non-covalently with a section of chromatin that is associated with gene promoter sequences of DNA.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0001077    transcriptional activator 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 activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
    GO:0001228    transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
    GO:0006977    DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle.
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0008015    blood circulation    The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
    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:0030030    cell projection organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0006884    cell volume homeostasis    Any process involved in maintaining the steady state of a cell's volume. The cell's volume refers to the three-dimensional space occupied by a cell.
    GO:0098534    centriole assembly    A cellular process that results in the assembly of one or more centrioles.
    GO:0002064    epithelial cell development    The process whose specific outcome is the progression of an epithelial cell over time, from its formation to the mature structure. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface.
    GO:0000278    mitotic cell cycle    Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
    GO:0044458    motile cilium assembly    The aggregation, arrangement and bonding together of a set of components to form a motile cilium.
    GO:1903251    multi-ciliated epithelial cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a multi-ciliated epithelial cell.
    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:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0008361    regulation of cell size    Any process that modulates the size of a cell.
    GO:0000083    regulation of transcription involved in G1/S transition of mitotic cell cycle    Any process that regulates transcription such that the target genes are involved in the transition between G1 and S phase of the mitotic cell cycle.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

Chain B   (TFDP2_HUMAN | Q14188)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000981    RNA polymerase II transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0003712    transcription cofactor activity    Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory 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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0006977    DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle.
    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:0000278    mitotic cell cycle    Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    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:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates 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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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

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

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        E2F4_HUMAN | Q16254: 5tuu

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