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(-) Description

Title :  SOLUTION STRUCTURE OF THE PDZ DOMAIN OF SPINOPHILIN/NEURABINII PROTEIN
 
Authors :  X. Qin, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  26 May 04  (Deposition) - 07 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Pdz Domain, Spinophilin/Neurabinii Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Qin, F. Hayashi, S. Yokoyama
Solution Structure Of The Pdz Domain Of Spinophilin/Neurabinii Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEURABIN-I
    Chains: A
    Engineered: YES
    Expression System Plasmid: P021030-40
    Expression System Vector Type: PLASMID
    Fragment: PDZ DOMAIN
    Gene: KAZUSA CNDA FH03567
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL FREE PROTEIN SYNTHESIS
    Synonym: SPINOPHILIN/NEURABINII, NEURAL TISSUE-SPECIFIC F- ACTIN BINDING PROTEIN I

 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 1WF8)

(-) Sites  (0, 0)

(no "Site" information available for 1WF8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WF8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WF8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WF8)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.NEB1_HUMAN504-592  1A:12-100

(-) Exons   (6, 6)

NMR Structure (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003406942aENSE00001518247chr7:94536949-9453701466NEB1_HUMAN-00--
1.5cENST000003406945cENSE00001379770chr7:94539210-945408201611NEB1_HUMAN1-4654651A:1-7 (gaps)48
1.6ENST000003406946ENSE00001793819chr7:94740571-94740703133NEB1_HUMAN466-510451A:8-1811
1.7ENST000003406947ENSE00001593289chr7:94750024-94750144121NEB1_HUMAN510-550411A:18-5841
1.8ENST000003406948ENSE00001679160chr7:94791179-94791283105NEB1_HUMAN550-585361A:58-9336
1.9ENST000003406949ENSE00001780046chr7:94827661-94827796136NEB1_HUMAN585-630461A:93-10210
1.11ENST0000034069411ENSE00001628822chr7:94855273-94855428156NEB1_HUMAN631-682521A:103-107 (gaps)8
1.12ENST0000034069412ENSE00001671576chr7:94876785-9487683854NEB1_HUMAN683-700180--
1.13ENST0000034069413ENSE00001714564chr7:94879338-94879567230NEB1_HUMAN701-777770--
1.14ENST0000034069414ENSE00001592551chr7:94881074-9488117097NEB1_HUMAN777-809330--
1.15ENST0000034069415ENSE00001720357chr7:94881271-94881442172NEB1_HUMAN810-867580--
1.16ENST0000034069416ENSE00001633288chr7:94897862-94898019158NEB1_HUMAN867-919530--
1.21ENST0000034069421ENSE00001039417chr7:94915518-94915637120NEB1_HUMAN920-959400--
1.22ENST0000034069422ENSE00001039430chr7:94916422-9491644524NEB1_HUMAN960-96780--
1.23ENST0000034069423ENSE00001039439chr7:94917848-94918030183NEB1_HUMAN968-1028610--
1.24eENST0000034069424eENSE00001390261chr7:94919403-949257256323NEB1_HUMAN1029-1098700--

(-) 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 A from PDB  Type:PROTEIN  Length:107
 aligned with NEB1_HUMAN | Q9ULJ8 from UniProtKB/Swiss-Prot  Length:1098

    Alignment length:237
                                   424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       
           NEB1_HUMAN   415 GETGTEQDEEEDSDENSYYQPDMEYSEIVGLPEEEEIPANRKIKFSSAPIKVFNTYSNEDYDRRNDEVDPVAASAEYELEKRVEKLELFPVELEKDEDGLGISIIGMGVGADAGLEKLGIFVKTVTEGGAAQRDGRIQVNDQIVEVDGISLVGVTQNFAATVLRNTKGNVRFVIGREKPGQVSEVAQLISQTLEQERRQRELLEQHYAQYDADDDETGEYATDEEEDEVGPVLPGSD 651
               SCOP domains -------------------------------------------------------------------------------------d1wf8a1 A:8-101 Neurabin-i                                                                    ---------------------------------------------------------- SCOP domains
               CATH domains 1wf8                                         A00                                      A:1-107  [code=2.30.42.10, no name defined]                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....-----------------------------------------...-------------------------------------eeeeeeeee.......eeeeeeee.......eeeeeeeee...hhhhhhh.......eeee..ee....hhhhhhhhhhhh..eeeeeeeee...-------------------------------------------------.---.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------PDZ  PDB: A:12-100 UniProt: 504-592                                                      ----------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5c  PDB: A:1-7 (gaps) UniProt: 1-465        Exon 1.6  PDB: A:8-18 UniProt: 466-510       ---------------------------------------Exon 1.8  PDB: A:58-93              ---------------------------------------------Exon 1.11             Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------Exon 1.7  PDB: A:18-58 UniProt: 510-550  ----------------------------------Exon 1.9  PDB: A:93-102 UniProt: 585-630      --------------------- Transcript 1 (2)
                 1wf8 A   1 GSSG-----------------------------------------SSG-------------------------------------LELFPVELEKDEDGLGISIIGMGVGADAGLEKLGIFVKTVTEGGAAQRDGRIQVNDQIVEVDGISLVGVTQNFAATVLRNTKGNVRFVIGREKPS-------------------------------------------------G---PSSG 107
                               |     -         -         -         -     | | -         -         -         -     |  12        22        32        42        52        62        72        82        92       102         -         -         -         -       103   |   
                               4                                         5 7                                     8                                                                                           102                                               103 104
   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)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WF8)

(-) Gene Ontology  (51, 51)

NMR Structure(hide GO term definitions)
Chain A   (NEB1_HUMAN | Q9ULJ8)
molecular function
    GO:0051020    GTPase binding    Interacting selectively and non-covalently with a GTPase, any enzyme that catalyzes the hydrolysis of GTP.
    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: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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0008157    protein phosphatase 1 binding    Interacting selectively and non-covalently with the enzyme protein phosphatase 1.
biological process
    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:0097237    cellular response to toxic substance    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 toxic stimulus.
    GO:0060079    excitatory postsynaptic potential    A process that leads to a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential.
    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:1900272    negative regulation of long-term synaptic potentiation    Any process that stops, prevents or reduces the frequency, rate or extent of long-term synaptic potentiation.
    GO:1904049    negative regulation of spontaneous neurotransmitter secretion    Any process that stops, prevents or reduces the frequency, rate or extent of spontaneous neurotransmitter secretion.
    GO:0051497    negative regulation of stress fiber assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of the assembly a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts.
    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:0048666    neuron development    The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
    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:0060999    positive regulation of dendritic spine development    Any process that increases the rate, frequency, or extent of dendritic spine development, the process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure.
    GO:1900454    positive regulation of long term synaptic depression    Any process that activates or increases the frequency, rate or extent of long term synaptic depression.
    GO:0010976    positive regulation of neuron projection development    Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is 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:0045860    positive regulation of protein kinase activity    Any process that activates or increases the frequency, rate or extent of protein kinase activity.
    GO:0030833    regulation of actin filament polymerization    Any process that modulates the frequency, rate or extent of the assembly of actin filaments by the addition of actin monomers to a filament.
    GO:0061001    regulation of dendritic spine morphogenesis    Any process that modulates the rate, frequency, or extent of dendritic spine morphogenesis, the process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
    GO:0051489    regulation of filopodium assembly    Any process that modulates the frequency, rate or extent of 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:0051963    regulation of synapse assembly    Any process that modulates the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
    GO:0051823    regulation of synapse structural plasticity    Any process that modulates the frequency, rate or extent of synapse structural plasticity. Synapse structural plasticity is a type of cytoskeletal remodeling; this remodeling is induced by stimuli that can lead to long term potentiation and it can be activity-dependent or -independent. Examples of cytoskeletal changes include the formation of new spines and increase in spine size; this can be accompanied by the insertion of greater numbers of glutamate (or other neurotransmitter) receptors into the post-synaptic membrane.
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: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: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: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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    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: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:1990761    growth cone lamellipodium    A thin sheetlike process extended by the leading edge of an axonal or dendritic growth cone; contains a dense meshwork of actin filaments.
    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:0031594    neuromuscular junction    The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential.
    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: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: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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