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(-) Description

Title :  STRUCTURAL BASIS OF PROSPERO-DNA INTERACTION; IMPLICATIONS FOR TRANSCRIPTION REGULATION IN DEVELOPING CELLS
 
Authors :  M. S. Yousef, B. W. Matthews
Date :  09 Oct 04  (Deposition) - 03 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Homeodomain, Protein-Dna Binding, Prospero, Neural Cell Development, Transcription Regulation/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. S. Yousef, B. W. Matthews
Structural Basis Of Prospero-Dna Interaction: Implications For Transcription Regulationin Developing Cells.
Structure V. 13 601 2005
PubMed-ID: 15837198  |  Reference-DOI: 10.1016/J.STR.2005.01.023
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*AP*GP*CP*AP*TP*GP*CP*CP*TP*G)-3'
    ChainsD
    EngineeredYES
    SyntheticYES
 
Molecule 2 - 5'-D(*CP*AP*GP*GP*CP*AP*TP*GP*CP*T)-3'
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 3 - PROTEIN PROSPERO
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentHOMEO-PROSPERO DOMAIN (RESIDUES 1245-1401)
    GenePROS
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ACD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1XPX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEO_PROSPEROPS51818 Homeo-Prospero domain profile.PROS_DROME1545-1703  1A:1245-1401

(-) Exons   (0, 0)

(no "Exon" information available for 1XPX)

(-) 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:144
 aligned with PROS_DROME | P29617 from UniProtKB/Swiss-Prot  Length:1703

    Alignment length:157
                                  1554      1564      1574      1584      1594      1604      1614      1624      1634      1644      1654      1664      1674      1684      1694       
          PROS_DROME   1545 SSTLTPMHLRKAKLMFFWVRYPSSAVLKMYFPDIKFNKNNTAQLVKWFSNFREFYYIQMEKYARQAVTEGIKTPDDLLIAGDSELYRVLNLHYNRNNHIEVPQNFRFVVESTLREFFRAIQGGKDTEQSWKKSIYKIISRMDDPVPEYFKSPNFLEQ 1701
               SCOP domains d1xpxa_ A: Homeo-prospero domain of Prospero protein                                                                                                          SCOP domains
               CATH domains 1xpxA00 A:1245-1401 Homeodomain-like (homeo-prospero domain)                                                                                                  CATH domains
               Pfam domains Prox1-1xpxA01 A:1245-1401                                                                                                                                     Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh......hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-------------hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HOMEO_PROSPERO  PDB: A:1245-1401 UniProt: 1545-1703                                                                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1xpx A 1245 SSTLTPMHLRKAKLMFFWVRYPSSAVLKMYFPDIKFNKNNTAQLVKWFSNFREFYYIQMEKYARQAVTE-------------SELYRVLNLHYNRNNHIEVPQNFRFVVESTLREFFRAIQGGKDTEQSWKKSIYKIISRMDDPVPEYFKSPNFLEQ 1401
                                  1254      1264      1274      1284      1294      1304        |-         -  |   1334      1344      1354      1364      1374      1384      1394       
                                                                                             1313          1327                                                                          

Chain C from PDB  Type:DNA  Length:10
                                           
                1xpx C  404 CAGGCATGCT  413
                                   413

Chain D from PDB  Type:DNA  Length:10
                                           
                1xpx D  300 AGCATGCCTG  309
                                   309

   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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (55, 55)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PROS_DROME | P29617)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0070314    G1 to G0 transition    A cell cycle arrest process that results in arrest during G1 phase, whereupon the cell enters a specialized resting state known as G0 or quiescence.
    GO:0007465    R7 cell fate commitment    The process in which the R7 photoreceptor commits to its cell fate. The R7 receptor contributes the central part of the rhabdomere in the apical parts of the ommatidium.
    GO:0008356    asymmetric cell division    The asymmetric division of cells to produce two daughter cells with different developmental potentials. It is of fundamental significance for the generation of cell diversity.
    GO:0055059    asymmetric neuroblast division    The process resulting in the physical partitioning and separation of a neuroblast into two daughter cells with different developmental potentials.
    GO:0055060    asymmetric neuroblast division resulting in ganglion mother cell formation    Any process resulting in the physical partitioning and separation of a neuroblast into a neuroblast and a ganglion mother cell.
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0007409    axonogenesis    De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon.
    GO:0060385    axonogenesis involved in innervation    The neurite development process that generates a long process of a neuron, as it invades a target tissue.
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0055007    cardiac muscle cell differentiation    The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction.
    GO:0045165    cell fate commitment    The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.
    GO:0001708    cell fate specification    The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    GO:0042676    compound eye cone cell fate commitment    The process in which the cone cells of the compound eye, the lens-secreting cells in the ommatidia, adopt pathways of differentiation that lead to the establishment of their distinct cell type.
    GO:0007619    courtship behavior    The behavioral interactions between organisms for the purpose of attracting sexual partners.
    GO:0070983    dendrite guidance    The process in which the migration of a dendrite is directed to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0048813    dendrite morphogenesis    The process in which the anatomical structures of a dendrite are generated and organized. A dendrite is a freely branching protoplasmic process of a nerve cell.
    GO:0001754    eye photoreceptor cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell, as found in the eye, the primary visual organ of most organisms.
    GO:0007402    ganglion mother cell fate determination    The cell fate determination process in which a cell becomes capable of differentiating autonomously into a ganglion mother cell regardless of its environment; upon determination, the cell fate cannot be reversed.
    GO:0010001    glial cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a glial cell.
    GO:0008049    male courtship behavior    The behavior of a male, for the purpose of attracting a sexual partner. An example of this process is found in Drosophila melanogaster.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0050771    negative regulation of axonogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of axonogenesis.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0007406    negative regulation of neuroblast proliferation    Any process that stops, prevents, or reduces the frequency, rate or extent of the proliferation of neuroblasts.
    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:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0007400    neuroblast fate determination    The cell fate determination process in which a cell becomes capable of differentiating autonomously into a neuroblast cell regardless of its environment; upon determination, the cell fate cannot be reversed. An example of this process is found in Mus musculus.
    GO:0007405    neuroblast proliferation    The expansion of a neuroblast population by cell division. A neuroblast is any cell that will divide and give rise to a neuron.
    GO:0007422    peripheral nervous system development    The process whose specific outcome is the progression of the peripheral nervous system over time, from its formation to the mature structure. The peripheral nervous system is one of the two major divisions of the nervous system. Nerves in the PNS connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
    GO:0006909    phagocytosis    An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    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:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    GO:0045676    regulation of R7 cell differentiation    Any process that modulates the frequency, rate or extent of R7 differentiation.
    GO:0045664    regulation of neuron differentiation    Any process that modulates the frequency, rate or extent of neuron differentiation.
    GO:1900180    regulation of protein localization to nucleus    Any process that modulates the frequency, rate or extent of protein localization to nucleus.
    GO:0042673    regulation of retinal cone cell fate specification    Any process that mediates the specification of a cell into a retinal cone cell.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007423    sensory organ development    The process whose specific outcome is the progression of sensory organs over time, from its formation to the mature structure.
    GO:0050909    sensory perception of taste    The series of events required for an organism to receive a gustatory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Gustation involves the direct detection of chemical composition, usually through contact with chemoreceptor cells. This is a neurological process.
    GO:0007416    synapse assembly    The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0007419    ventral cord development    The process whose specific outcome is the progression of the ventral cord over time, from its formation to the mature structure. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms.
cellular component
    GO:0045179    apical cortex    The region that lies just beneath the plasma membrane on the apical edge of a cell.
    GO:0045180    basal cortex    The region that lies just beneath the plasma membrane on the basal edge of a cell.
    GO:0045178    basal part of cell    The region of a cell situated near the base. For example, in a polarized epithelial cell, the basal surface rests on the basal lamina that separates the epithelium from other tissue.
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    GO:0005875    microtubule associated complex    Any multimeric complex connected to a microtubule.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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        PROS_DROME | P296171mij

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