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(-) Description

Title :  SOLUTION STRUCTURE OF THE FIRST PDZ DOMAIN OF AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING FAMILY A, MEMBER 1
 
Authors :  X. R. Qin, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  13 May 05  (Deposition) - 13 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Pdz Domain, Amyloid Beta A4 Precursor Protein-Binding Family A, Member 1, Neuron-Specific Xii Protein, Adapter Protein Xii Alpha, Neuronal Munc 18-1-Interacting Protein 1 Mint-1, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. R. Qin, F. Hayashi, S. Yokoyama
Solution Structure Of The First Pdz Domain Of Amyloid Beta A4 Precursor Protein-Binding Family A, Member 1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMYLOID BETA (A4) PRECURSOR PROTEIN-BINDING, FAMILY A, MEMBER 1 (X11)
    ChainsA
    EngineeredYES
    Expression System PlasmidP050118-02
    Expression System Vector TypePLASMID
    FragmentPDZ DOMAIN
    GeneAPBA1, MINT1, X11
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymNEURON-SPECIFIC XII PROTEIN, NEURONAL MUNC18-1- INTERACTING PROTEIN 1, MINT-1, ADAPTER PROTEIN X11 ALPHA

 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 1X45)

(-) Sites  (0, 0)

(no "Site" information available for 1X45)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X45)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X45)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X45)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.APBA1_HUMAN656-741
747-823
  2A:8-92
A:98-98

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002653811ENSE00001228144chr9:72287222-72287069154APBA1_HUMAN-00--
1.2ENST000002653812ENSE00001089894chr9:72132195-721309271269APBA1_HUMAN1-4004000--
1.3ENST000002653813ENSE00001089895chr9:72091059-7209096496APBA1_HUMAN401-432320--
1.4ENST000002653814ENSE00001089892chr9:72086611-7208657240APBA1_HUMAN433-446140--
1.5aENST000002653815aENSE00000982740chr9:72082884-72082739146APBA1_HUMAN446-494490--
1.6ENST000002653816ENSE00001015445chr9:72073104-7207307233APBA1_HUMAN495-505110--
1.7ENST000002653817ENSE00000982741chr9:72072055-7207196987APBA1_HUMAN506-534290--
1.8bENST000002653818bENSE00000917481chr9:72071348-72071163186APBA1_HUMAN535-596620--
1.9ENST000002653819ENSE00000982742chr9:72067217-72067038180APBA1_HUMAN597-656601A:1-88
1.10ENST0000026538110ENSE00000982743chr9:72064712-72064500213APBA1_HUMAN657-727711A:9-7971
1.11ENST0000026538111ENSE00000982744chr9:72056031-72055912120APBA1_HUMAN728-767401A:80-98 (gaps)39
1.12ENST0000026538112ENSE00000982745chr9:72047592-72047452141APBA1_HUMAN768-814470--
1.13ENST0000026538113ENSE00001228156chr9:72046314-720452041111APBA1_HUMAN815-837230--

(-) 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:98
 aligned with APBA1_HUMAN | Q02410 from UniProtKB/Swiss-Prot  Length:837

    Alignment length:118
                                   658       668       678       688       698       708       718       728       738       748       758        
          APBA1_HUMAN   649 SKSENCKDVFIEKQKGEILGVVIVESGWGSILPTVIIANMMHGGPAEKSGKLNIGDQIMSINGTSLVGLPLSTCQSIIKGLKNQSRVKLNIVRCPPVTTVLIRRPDLRYQLGFSVQNG 766
               SCOP domains -------d1x45a1 A:8-92                                                                       -------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------PDZ-1x45A01 A:8-92                                                                   -------------------------- Pfam domains
         Sec.struct. author .......eeeee........eeee...........eeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhh.....eeeeeee...--------------------... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------PDZ  PDB: A:8-92 UniProt: 656-741                                                     -----PDZ  PDB: A:98-98    PROSITE
               Transcript 1 Exon 1.9Exon 1.10  PDB: A:9-79 UniProt: 657-727                                Exon 1.11  PDB: A:80-98 (gaps)          Transcript 1
                 1x45 A   1 GSSGSSGDVFIEKQKGEILGVVIVESGWGSILPTVIIANMMHGGPAEKSGKLNIGDQIMSINGTSLVGLPLSTCQSIIKGLKNQSRVKLNIVSGP--------------------SSG  98
                                    10        20        30        40        50        60        70        80        90    |    -         -     |  
                                                                                                                         95                   96  

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X45)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: PDZ-like (184)

(-) Gene Ontology  (30, 30)

NMR Structure(hide GO term definitions)
Chain A   (APBA1_HUMAN | Q02410)
molecular function
    GO:0030165    PDZ domain binding    Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
    GO:0001540    amyloid-beta binding    Interacting selectively and non-covalently with amyloid-beta peptide/protein and/or its precursor.
    GO:0005546    phosphatidylinositol-4,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions.
    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).
biological process
    GO:0008088    axo-dendritic transport    The directed movement of organelles or molecules along microtubules in neuron projections.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0014051    gamma-aminobutyric acid secretion    The regulated release of gamma-aminobutyric acid by a cell or a tissue. The gamma-aminobutyric acid is the principal inhibitory neurotransmitter in the brain but is also found in several extraneural tissues.
    GO:0014047    glutamate secretion    The controlled release of glutamate by a cell. The glutamate is the most abundant excitatory neurotransmitter in the nervous system.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    GO:0007626    locomotory behavior    The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    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:0007269    neurotransmitter secretion    The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium regualated exocytosis during synaptic transmission.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0010468    regulation of gene expression    Any process that modulates 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:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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: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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0008021    synaptic vesicle    A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        APBA1_HUMAN | Q024101aqc 1u37 1u38 1u39 1u3b 1x11 1y7n

(-) Related Entries Specified in the PDB File

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