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(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURE OF THE EGF DOMAIN OF SPITZ
 
Authors :  D. E. Klein, S. E. Stayrook, M. A. Lemmon
Date :  19 Feb 08  (Deposition) - 20 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Spitz, Argos, Egf, Developmental Protein, Differentiation, Egf-Like Domain, Endoplasmic Reticulum, Glycoprotein, Golgi Apparatus, Membrane, Neurogenesis, Transmembrane, Hormone/Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. E. Klein, S. E. Stayrook, F. Shi, K. Narayan, M. A. Lemmon
Structural Basis For Egfr Ligand Sequestration By Argos.
Nature V. 453 1271 2008
PubMed-ID: 18500331  |  Reference-DOI: 10.1038/NATURE06978
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN SPITZ
    ChainsA
    EngineeredYES
    Expression SystemDROSOPHILA MELANOGASTER
    Expression System CellSCHNEIDER-2 CELLS
    Expression System PlasmidPMT/BIP/V5-HISA(INVITROGEN)
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 76-127
    GeneSPI
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3CA7)

(-) Sites  (0, 0)

(no "Site" information available for 3CA7)

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:54 -A:69
2A:63 -A:82
3A:84 -A:93

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CA7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CA7)

(-) PROSITE Motifs  (3, 2)

Asymmetric/Biological Unit (3, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EGF_3PS50026 EGF-like domain profile.SPITZ_DROME78-122  1A:50-94
2EGF_1PS00022 EGF-like domain signature 1.SPITZ_DROME110-121  1A:82-93
3EGF_2PS01186 EGF-like domain signature 2.SPITZ_DROME110-121  1A:82-93

(-) Exons   (0, 0)

(no "Exon" information available for 3CA7)

(-) 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:50
 aligned with SPITZ_DROME | Q01083 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:50
                                    85        95       105       115       125
          SPITZ_DROME    76 TFPTYKCPETFDAWYCLNDAHCFAVKIADLPVYSCECAIGFMGQRCEYKE 125
               SCOP domains -------------------------------------------------- SCOP domains
               CATH domains 3ca7A00 A:48-97 Laminin                            CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhh.....eeeeeee..eeeeeee....ee.....ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --EGF_3  PDB: A:50-94 UniProt: 78-122          --- PROSITE (1)
                PROSITE (2) ----------------------------------EGF_2       ---- PROSITE (2)
                PROSITE (3) ----------------------------------EGF_1       ---- PROSITE (3)
                 Transcript -------------------------------------------------- Transcript
                 3ca7 A  48 TFPTYKCPETFDAWYCLNDAHCFAVKIADLPVYSCECAIGFMGQRCEYKE  97
                                    57        67        77        87        97

   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 3CA7)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CA7)

(-) Gene Ontology  (39, 39)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SPITZ_DROME | Q01083)
molecular function
    GO:0005154    epidermal growth factor receptor binding    Interacting selectively and non-covalently with the epidermal growth factor receptor.
    GO:0008317    gurken receptor binding    Interacting selectively and non-covalently with the gurken growth factor receptor.
    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).
biological process
    GO:0000086    G2/M transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
    GO:0045470    R8 cell-mediated photoreceptor organization    The regionalization process that coordinates the recruitment and organization of other non-R8 photoreceptors by the R8 photoreceptor.
    GO:0048149    behavioral response to ethanol    Any process that results in a change in the behavior of an organism as a result of an ethanol stimulus.
    GO:0007298    border follicle cell migration    The directed movement of a border cell through the nurse cells to reach the oocyte. An example of this is found in Drosophila melanogaster.
    GO:0046845    branched duct epithelial cell fate determination, open tracheal system    Allocation of a set number of cells to each primary branch in an open tracheal system, prior to the onset of cell migration. This establishes different domains of cells within the tracheal placode.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0035225    determination of genital disc primordium    Allocation of embryonic cells to the genital imaginal disc founder populations. Early in development at the blastoderm stage, the anlage of the genital disc of both sexes consists of three primordia: the female genital primoridum lcoated anteriorly, the anal primoridum located posteriorly, and the male gential primordium between the two.
    GO:0007173    epidermal growth factor receptor signaling pathway    A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0061331    epithelial cell proliferation involved in Malpighian tubule morphogenesis    The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population and contributing to the shaping of a Malpighian tubule.
    GO:0003015    heart process    A circulatory system process carried out by the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0007476    imaginal disc-derived wing morphogenesis    The process in which the anatomical structures of the imaginal disc-derived wing are generated and organized. The wing is an appendage modified for flying.
    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:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0046673    negative regulation of compound eye retinal cell programmed cell death    Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death that occurs in the compound eye retina.
    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:0022008    neurogenesis    Generation of cells within the nervous system.
    GO:0007438    oenocyte development    The process whose specific outcome is the progression of the oenocyte over time, from its formation to the mature structure. The oenocytes are large secretory cells found in clusters underlying the epidermis of larval abdominal segments.
    GO:0008355    olfactory learning    Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs in response to (repeated) exposure to an olfactory cue.
    GO:0007424    open tracheal system development    The process whose specific outcome is the progression of an open tracheal system over time, from its formation to the mature structure. An open tracheal system is a respiratory system, a branched network of epithelial tubes that supplies oxygen to target tissues via spiracles. An example of this is found in Drosophila melanogaster.
    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:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0045742    positive regulation of epidermal growth factor receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
    GO:0050769    positive regulation of neurogenesis    Any process that activates or increases the frequency, rate or extent of neurogenesis, the origin and formation of neurons.
    GO:0007432    salivary gland boundary specification    Determination of where the salivary gland forms, the total number of salivary gland cells and how many cells are allocated to each of the specialised cell types within the salivary gland.
    GO:0016330    second mitotic wave involved in compound eye morphogenesis    A discrete cell cycle in the third instar eye imaginal disc after progression of the morphogenetic furrow that contributes to compound eye morphogenesis. It is essential for generation of a sufficient pool of uncommitted cells to develop complete ommatidia.
    GO:0035277    spiracle morphogenesis, open tracheal system    The process in which the anatomical structures of a spiracle are generated and organized. Spiracles are the openings in the insect open tracheal system; externally they connect to the epidermis and internally they connect to the tracheal trunk.
    GO:0048865    stem cell fate commitment    The process in which the developmental fate of a cell becomes restricted such that it will develop into a stem cell.
    GO:0007421    stomatogastric nervous system development    The process whose specific outcome is the progression of the stomatogastric nervous system over time, from its formation to the mature structure.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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

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

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        SPITZ_DROME | Q010833c9a 3ltf 3ltg

(-) Related Entries Specified in the PDB File

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