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(-) Description

Title :  THE PTB DOMAIN OF MINT1 IS AUTOINHIBITED BY A HELIX IN THE C-TERMINAL LINKER REGION
 
Authors :  D. R. Tomchick, J. Rizo, A. Ho, Y. Xu
Date :  13 Jan 12  (Deposition) - 07 Mar 12  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  X11S/Mints, Ptb Domain, Chimera Protein, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. F. Matos, Y. Xu, I. Dulubova, Z. Otwinowski, J. M. Richardson, D. R. Tomchick, J. Rizo, A. Ho
Autoinhibition Of Mint1 Adaptor Protein Regulates Amyloid Precursor Protein Binding And Processing.
Proc. Natl. Acad. Sci. Usa V. 109 3802 2012
PubMed-ID: 22355143  |  Reference-DOI: 10.1073/PNAS.1119075109

(-) Compounds

Molecule 1 - AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING FAMILY A MEMBER 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentPTB DOMAIN, UNP RESIDUES 453-643 WITH DELETION OF RESIDUES 497-508
    GeneAPBA1, MINT1, X11
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymADAPTER PROTEIN X11ALPHA,NEURON-SPECIFIC X11 PROTEIN, NEURONAL MUNC18-1-INTERACTING PROTEIN 1,MINT-1,ADAPTER PROTEIN X11ALPHA,NEURON-SPECIFIC X11 PROTEIN,NEURONAL MUNC18-1-INTERACTING PROTEIN 1,MINT-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2CL1Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
4IPA2Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:524BINDING SITE FOR RESIDUE CL A 701
2AC2SOFTWAREASP A:459 , GLN A:487 , GLU A:490 , HOH A:803 , HOH A:851BINDING SITE FOR RESIDUE ACY A 702
3AC3SOFTWAREHIS A:542 , ARG A:563 , ARG A:564 , HOH A:867BINDING SITE FOR RESIDUE ACY A 703
4AC4SOFTWAREILE A:458 , ILE A:523 , GLN A:608BINDING SITE FOR RESIDUE IPA A 704
5AC5SOFTWAREVAL A:492 , SER A:493 , HOH A:853BINDING SITE FOR RESIDUE IPA A 705
6AC6SOFTWARELEU A:468 , GLY A:469 , SER A:470 , ALA A:491 , ILE A:495BINDING SITE FOR RESIDUE GOL A 706
7AC7SOFTWAREPRO A:543 , ARG A:545BINDING SITE FOR RESIDUE GOL A 707

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DBB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DBB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DBB)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PIDPS01179 Phosphotyrosine interaction domain (PID) profile.APBA1_RAT459-645  1A:459-640

(-) Exons   (0, 0)

(no "Exon" information available for 4DBB)

(-) 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:150
 aligned with APBA1_RAT | O35430 from UniProtKB/Swiss-Prot  Length:839

    Alignment length:186
                                   464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634      
            APBA1_RAT   455 EDLIDGIIFAANYLGSTQLLSDKTPSKNVRMMQAQEAVSRIKTAQKLAKSRKKAPEGESQPMTEVDLFISTQRIKVLNADTQEPMMDHPLRTISYIADIGNIVVLMARRRMPRSNSQENVEASHPSQDAKRQYKMICHVFESEDAQLIAQSIGQAFSVAYQEFLRANGINPEDLSQKEYSDLLNTQ 640
               SCOP domains d4dbba_ A: automated matches                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeeeeeeeeee....hhhhhhhhhhhhhhh..-----------------...eeeeeeee..eeeeee.....eeeeee...eeeeeee..eeeeeeee.....-----------------.eeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..--.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----PID  PDB: A:459-640 UniProt: 459-645                                                                                                                                                   PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dbb A 455 EDLIDGIIFAANYLGSTQLLSDKTPSKNVRMMQAQEAVSRIK-----------------QPMTEVDLFISTQRIKVLNADTQEPMMDHPLRTISYIADIGNIVVLMARRRMPRS-----------------QYKMICHVFESEDAQLIAQSIGQAFSVAYQEFLRA--INPEDLSQKEYSDLLNTQ 640
                                   464       474       484       494 |       -       514       524       534       544       554       564   |     -         - |     594       604       614     | 624       634      
                                                                   496               514                                                   568               586                               620  |                 
                                                                                                                                                                                                  623                 

   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "CATH Domain" information available for 4DBB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DBB)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (APBA1_RAT | O35430)
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: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: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:0016079    synaptic vesicle exocytosis    Fusion of intracellular membrane-bounded vesicles with the pre-synaptic membrane of the neuronal cell resulting in release of neurotransmitter into the synaptic cleft.
    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: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: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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