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(-) Description

Title :  SPINOPHILIN PDZ DOMAIN
 
Authors :  M. S. Kelker, W. Peti
Date :  23 Feb 06  (Deposition) - 09 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  B  (20x)
Keywords :  Spinophilin, Pdz Domain, Cns, Synaptic Transmission, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. S. Kelker, B. Dancheck, T. Ju, R. P. Kessler, J. Hudak, A. C. Nairn, W. Peti
Structural Basis For Spinophilin-Neurabin Receptor Interaction.
Biochemistry V. 46 2333 2007
PubMed-ID: 17279777  |  Reference-DOI: 10.1021/BI602341C
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEURABIN-2
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidDERIVITIVE OF PET28A
    Expression System StrainBL21 (DE3) RIL CODON PLUS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentPDZ DOMAIN
    GenePPP1R9B
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymNEURABIN-II, NEURAL TISSUE-SPECIFIC F-ACTIN BINDING PROTEIN II, PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 9B, SPINOPHILIN, P130, PP1BP134

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2G5M)

(-) Sites  (0, 0)

(no "Site" information available for 2G5M)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2G5M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2G5M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2G5M)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.NEB2_RAT496-584  1B:7-95

(-) Exons   (0, 0)

(no "Exon" information available for 2G5M)

(-) Sequences/Alignments

NMR Structure
   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 B from PDB  Type:PROTEIN  Length:113
 aligned with NEB2_RAT | O35274 from UniProtKB/Swiss-Prot  Length:817

    Alignment length:113
                                   499       509       519       529       539       549       559       569       579       589       599   
             NEB2_RAT   490 ERLELFPVELEKDSEGLGISIIGMGAGADMGLEKLGIFVKTVTEGGAAHRDGRIQVNDLLVEVDGTSLVGVTQSFAASVLRNTKGRVRFMIGRERPGEQSEVAQLIQQTLEQE 602
               SCOP domains d2g5mb_ B: automated matches                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..........eeeeee.........eeeeeee....hhhhhhh.......eeee..ee....hhhhhhhhhhhh....eeeeee.................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------PDZ  PDB: B:7-95 UniProt: 496-584                                                        ------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2g5m B   1 GHMELFPVELEKDSEGLGISIIGMGAGADMGLEKLGIFVKTVTEGGAAHRDGRIQVNDLLVEVDGTSLVGVTQSFAASVLRNTKGRVRFMIGRERPGEQSEVAQLIQQTLEQE 113
                                    10        20        30        40        50        60        70        80        90       100       110   

   Legend:   → Mismatch (orange background)
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    → 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)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2G5M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G5M)

(-) Gene Ontology  (82, 82)

NMR Structure(hide GO term definitions)
Chain B   (NEB2_RAT | O35274)
molecular function
    GO:0031749    D2 dopamine receptor binding    Interacting selectively and non-covalently with a D2 dopamine receptor.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0051015    actin filament binding    Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
    GO:0044325    ion channel binding    Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
    GO:0019900    kinase binding    Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0008157    protein phosphatase 1 binding    Interacting selectively and non-covalently with the enzyme protein phosphatase 1.
    GO:0004864    protein phosphatase inhibitor activity    Stops, prevents or reduces the activity of a protein phosphatase, an enzyme that hydrolyzes phosphate groups from phosphorylated proteins.
biological process
    GO:0030042    actin filament depolymerization    Disassembly of actin filaments by the removal of actin monomers from a filament.
    GO:0007015    actin filament organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0019722    calcium-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions.
    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:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0035690    cellular response to drug    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0071364    cellular response to epidermal growth factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an epidermal growth factor stimulus.
    GO:0071392    cellular response to estradiol stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0071482    cellular response to light stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
    GO:0071315    cellular response to morphine    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a morphine stimulus. Morphine is an opioid alkaloid, isolated from opium, with a complex ring structure.
    GO:0071407    cellular response to organic cyclic compound    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:1901653    cellular response to peptide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide stimulus.
    GO:0021987    cerebral cortex development    The progression of the cerebral cortex over time from its initial formation until its mature state. The cerebral cortex is the outer layered region of the telencephalon.
    GO:0016358    dendrite development    The process whose specific outcome is the progression of the dendrite over time, from its formation to the mature structure. A dendrite is a freely branching protoplasmic process of a nerve cell.
    GO:0003006    developmental process involved in reproduction    A developmental process in which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring.
    GO:0046847    filopodium assembly    The assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.
    GO:0021766    hippocampus development    The progression of the hippocampus over time from its initial formation until its mature state.
    GO:0007612    learning    Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.
    GO:0060179    male mating behavior    The specific behavior of a male organism that is associated with reproduction.
    GO:0050804    modulation of chemical synaptic transmission    Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission.
    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:0032515    negative regulation of phosphoprotein phosphatase activity    Any process that stops or reduces the activity of a phosphoprotein phosphatase.
    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:0031175    neuron projection development    The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:1903829    positive regulation of cellular protein localization    Any process that activates or increases the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
    GO:0090004    positive regulation of establishment of protein localization to plasma membrane    Any process that increases the frequency, rate or extent of the directed movement of a protein to a specific location in the plasma membrane.
    GO:1904372    positive regulation of protein localization to actin cortical patch    Any process that activates or increases the frequency, rate or extent of protein localization to actin cortical patch.
    GO:1903119    protein localization to actin cytoskeleton    A process in which a protein is transported to, or maintained in, the location of an actin cytoskeleton.
    GO:1990778    protein localization to cell periphery    A process in which a protein is transported to, or maintained in, the cell periphery.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:2000474    regulation of opioid receptor signaling pathway    Any process that modulates the frequency, rate or extent of opioid receptor signaling pathway.
    GO:0001932    regulation of protein phosphorylation    Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein.
    GO:0061458    reproductive system development    The progression of the reproductive system over time from its formation to the mature structure. The reproductive system consists of the organs that function in reproduction.
    GO:1904386    response to L-phenylalanine derivative    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a L-phenylalanine derivative stimulus.
    GO:0043200    response to amino acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
    GO:0001975    response to amphetamine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amphetamine stimulus. Amphetamines consist of a group of compounds related to alpha-methylphenethylamine.
    GO:0097338    response to clozapine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a clozapine stimulus.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0032355    response to estradiol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0035902    response to immobilization stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of being rendered immobile.
    GO:1904373    response to kainic acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a kainic acid stimulus.
    GO:0035094    response to nicotine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nicotine stimulus.
    GO:0014070    response to organic cyclic compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0010243    response to organonitrogen compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
    GO:0034695    response to prostaglandin E    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a prostagladin E stimulus.
    GO:0048545    response to steroid hormone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005912    adherens junction    A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0030864    cortical actin cytoskeleton    The portion of the actin cytoskeleton, comprising filamentous actin and associated proteins, that lies just beneath the plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:1990780    cytoplasmic side of dendritic spine plasma membrane    The leaflet of the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface surrounding a dendritic spine.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    GO:0044327    dendritic spine head    Distal part of the dendritic spine, that carries the post-synaptic density.
    GO:0032591    dendritic spine membrane    The portion of the plasma membrane surrounding a dendritic spine.
    GO:0044326    dendritic spine neck    Part of the dendritic spine that connects the dendritic shaft to the head of the dendritic spine.
    GO:0030175    filopodium    Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    GO:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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.
    GO:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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 Related Entries

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

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        NEB2_RAT | O352743egg 3egh

(-) Related Entries Specified in the PDB File

6927 SPINOPHILIN PDZ DOMAIN PEAK LISTS
6933 NEURABIN PDZ DOMAIN PEAK LISTS
2fn5 NEURABIN PDZ DOMAIN COORDINATES