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(-) Description

Title :  THE FIRST C2 DOMAIN OF HUMAN SYNAPTOTAGMIN XIII
 
Authors :  T. Nagashima, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  26 May 04  (Deposition) - 26 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  C2 Domain, Exocytosis, Neurotransmitter Release, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Nagashima, F. Hayashi, S. Yokoyama
The First C2 Domain Of Human Synaptotagmin Xiii
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SYNAPTOTAGMIN XIII
    Chains: A
    Engineered: YES
    Expression System Plasmid: P040113-87
    Expression System Vector Type: PLASMID
    Fragment: C2 DOMAIN
    Gene: KAZUSA CDNA FH02770
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS

 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 1WFM)

(-) Sites  (0, 0)

(no "Site" information available for 1WFM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WFM)

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000000209261aENSE00000711706chr11:45307870-45307576295SYT13_HUMAN1-61610--
1.5ENST000000209265ENSE00000711692chr11:45277442-45277217226SYT13_HUMAN62-137760--
1.6ENST000000209266ENSE00000711656chr11:45275955-45275821135SYT13_HUMAN137-182461A:1-3535
1.7bENST000000209267bENSE00000711649chr11:45274273-45273972302SYT13_HUMAN182-2821011A:35-134100
1.8ENST000000209268ENSE00000711642chr11:45268063-45267934130SYT13_HUMAN283-326441A:135-1384
1.9bENST000000209269bENSE00001329248chr11:45265907-452618524056SYT13_HUMAN326-4261010--

(-) 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:138
 aligned with SYT13_HUMAN | Q7L8C5 from UniProtKB/Swiss-Prot  Length:426

    Alignment length:140
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287
          SYT13_HUMAN   148 WNPEKAASWNQAPKLHYCLDYDCQKAELFVTRLEAVTSNHDGGCDCYVQGSVANRTGSVEAQTALKKRQLHTTWEEGLVLPLAEEELPTATLTLTLRTCDRFSRHSVAGELRLGLDGTSVPLGAAQWGELKTSAKEPSAG 287
               SCOP domains d1wfma_ A: Synaptotagmin XIII                                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeee.....eeeeeeeeee.........eeeeeeeee..eeeeee.........ee....eeee.........eeeeeeee..........eeeeee...........eeee.....--.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: A:1-35 [INCOMPLETE] ----------------------------------------------------------------------------------------------------1.8   Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.7b  PDB: A:35-134 UniProt: 182-282 [INCOMPLETE]                                               ----- Transcript 1 (2)
                 1wfm A   1 GSSGSSGSWNQAPKLHYCLDYDCQKAELFVTRLEAVTSNHDGGCDCYVQGSVANRTGSVEAQTALKKRQLHTTWEEGLVLPLAEEELPTATLTLTLRTCDRFSRHSVAGELRLGLDGTSVPLGAAQWGELKTSG--PSSG 138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   |  |138
                                                                                                                                                               134  |   
                                                                                                                                                                  135
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  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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A   (SYT13_HUMAN | Q7L8C5)
molecular function
    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: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: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.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0030133    transport vesicle    Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.

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