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(-) Description

Title :  SOLUTION STRUCTURE OF THE RING DOMAIN OF THE SYNAPTOTAGMIN-LIKE PROTEIN 4
 
Authors :  K. Miyamoto, M. Sato, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  23 May 05  (Deposition) - 23 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Exophilin 2, Granuphilin, Synaptotagmin-Like Protein 4, Ring Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Miyamoto, M. Sato, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Ring Domain Of The Synaptotagmin-Like Protein 4
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SYNAPTOTAGMIN-LIKE PROTEIN 4
    ChainsA
    EngineeredYES
    Expression System PlasmidP041101-16
    Expression System Vector TypePLASMID
    FragmentRING DOMAIN
    GeneSYTL4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymEXOPHILIN 2, GRANUPHILIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:28 , CYS A:31 , CYS A:53 , CYS A:56BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS A:45 , CYS A:48 , CYS A:67 , CYS A:70BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CSZ)

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003729892bENSE00001459253X:99986498-9998640693SYTL4_HUMAN-00--
1.3aENST000003729893aENSE00001459251X:99959882-9995980776SYTL4_HUMAN-00--
1.4ENST000003729894ENSE00001796780X:99958181-9995808993SYTL4_HUMAN-00--
1.5bENST000003729895bENSE00001382017X:99957103-99956924180SYTL4_HUMAN1-37371A:1-55
1.6ENST000003729896ENSE00001154545X:99956669-99956454216SYTL4_HUMAN37-109731A:6-7166
1.7ENST000003729897ENSE00001154536X:99956325-99956216110SYTL4_HUMAN109-146381A:72-765
1.8ENST000003729898ENSE00001154529X:99955995-99955893103SYTL4_HUMAN146-180350--
1.9ENST000003729899ENSE00001304452X:99946206-99946105102SYTL4_HUMAN180-214350--
1.10ENST0000037298910ENSE00000673591X:99945635-9994556076SYTL4_HUMAN214-239260--
1.11ENST0000037298911ENSE00000673572X:99945162-9994507291SYTL4_HUMAN240-270310--
1.12ENST0000037298912ENSE00000673564X:99944956-99944853104SYTL4_HUMAN270-304350--
1.13aENST0000037298913aENSE00000673560X:99943440-9994334893SYTL4_HUMAN305-335310--
1.13dENST0000037298913dENSE00000673548X:99942242-99942064179SYTL4_HUMAN336-395600--
1.13eENST0000037298913eENSE00000673528X:99941778-99941676103SYTL4_HUMAN395-429350--
1.13fENST0000037298913fENSE00001218079X:99941148-99940987162SYTL4_HUMAN430-483540--
1.14ENST0000037298914ENSE00001217979X:99936332-99936224109SYTL4_HUMAN484-520370--
1.15ENST0000037298915ENSE00001217969X:99934409-99934310100SYTL4_HUMAN520-553340--
1.16bENST0000037298916bENSE00000673492X:99933596-99933388209SYTL4_HUMAN553-623710--
1.17cENST0000037298917cENSE00001459238X:99931173-999294881686SYTL4_HUMAN623-671490--

(-) 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:76
 aligned with SYTL4_HUMAN | Q96C24 from UniProtKB/Swiss-Prot  Length:671

    Alignment length:88
                                    38        48        58        68        78        88        98       108        
          SYTL4_HUMAN    29 RKADEKRIRRLKNELLEIKRKGAKRGSQHYSDRTCARCQESLGRLSPKTNTCRGCNHLVCRDCRIQESNGTWRCKVCAKEIELKKATG 116
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....-------......................................ee....ee.....eee.....eeehhhh-----..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5b-----------------------------------------------------------------------Exon 1.7 Transcript 1 (1)
           Transcript 1 (2) --------Exon 1.6  PDB: A:6-71 UniProt: 37-109 [INCOMPLETE]                       ------- Transcript 1 (2)
                 2csz A   1 GSSGS-------SGLLEIKRKGAKRGSQHYSDRTCARCQESLGRLSPKTNTCRGCNHLVCRDCRIQESNGTWRCKVCS-----GPSSG  76
                                |    -  |     13        23        33        43        53        63       | -   |    
                                5       6                                                               71    72    

   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 2CSZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

NMR Structure(hide GO term definitions)
Chain A   (SYTL4_HUMAN | Q96C24)
molecular function
    GO:0017137    Rab GTPase binding    Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0005544    calcium-dependent phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester, in the presence of calcium.
    GO:0030276    clathrin binding    Interacting selectively and non-covalently with a clathrin heavy or light chain, the main components of the coat of coated vesicles and coated pits, and which also occurs in synaptic vesicles.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0042043    neurexin family protein binding    Interacting selectively and non-covalently with neurexins, synaptic cell surface proteins related to latrotoxin receptor, laminin and agrin. Neurexins act as cell recognition molecules at nerve terminals.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    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:0019905    syntaxin binding    Interacting selectively and non-covalently with a syntaxin, a SNAP receptor involved in the docking of synaptic vesicles at the presynaptic zone of a synapse.
biological process
    GO:0048791    calcium ion-regulated exocytosis of neurotransmitter    The release of a neurotransmitter into the synaptic cleft by exocytosis of synaptic vesicles, where the release step is dependent on a rise in cytosolic calcium ion levels.
    GO:0006887    exocytosis    A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
    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:0071985    multivesicular body sorting pathway    A vesicle-mediated transport process in which transmembrane proteins are ubiquitylated to facilitate their entry into luminal vesicles of multivesicular bodies (MVBs); upon subsequent fusion of MVBs with lysosomes or vacuoles, the cargo proteins are degraded.
    GO:0046676    negative regulation of insulin secretion    Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of insulin.
    GO:0045921    positive regulation of exocytosis    Any process that activates or increases the frequency, rate or extent of exocytosis.
    GO:0050714    positive regulation of protein secretion    Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell.
    GO:0017158    regulation of calcium ion-dependent exocytosis    Any process that modulates the frequency, rate or extent of calcium ion-dependent exocytosis.
    GO:0006906    vesicle fusion    Fusion of the membrane of a transport vesicle with its target membrane.
cellular component
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0070382    exocytic vesicle    A transport vesicle that mediates transport from an intracellular compartment to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis.
    GO:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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:0098793    presynapse    The part of a synapse that is part of the presynaptic cell.
    GO:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.
    GO:0030667    secretory granule membrane    The lipid bilayer surrounding a secretory granule.
    GO:0030658    transport vesicle membrane    The lipid bilayer surrounding a transport vesicle.

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        SYTL4_HUMAN | Q96C243fdw

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