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NMR Structure - model 1  (Jmol Viewer)
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(-) Description

Authors :  M. Yoneyama, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  02 May 05  (Deposition) - 02 Nov 05  (Release) - 24 Feb 09  (Revision)
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Synapse Associated Protein 1, Bsd Domain, Homolog Of The Drosophila Sap47, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  M. Yoneyama, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Bsd Domain Of Human Synapse Associated Protein 1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

    Expression System PlasmidP040531-07
    Expression System Vector TypePLASMID
    FragmentBSD DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 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 1X3A)

(-) Sites  (0, 0)

(no "Site" information available for 1X3A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X3A)

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Val A:67 -Pro A:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X3A)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
1BSDPS50858 BSD domain profile.SYAP1_HUMAN158-210  1A:36-88

(-) Exons   (4, 4)

NMR Structure (4, 4)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003801552ENSE00001150620X:16753350-16753468119SYAP1_HUMAN59-98401A:2-7 (gaps)30
1.6ENST000003801556ENSE00001150594X:16773068-16773216149SYAP1_HUMAN192-242511A:70-100 (gaps)42

(-) 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:100
 aligned with SYAP1_HUMAN | Q96A49 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:176
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227      
               SCOP domains ------------------------------------------------------------------------d1x3aa1 A:8-94 Synapse associated protein 1, SYAP1                                     ----------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------BSD-1x3aA01 A:33-94                                           ----------------- Pfam domains
         Sec.struct. author .------.....------------------------.-----------------------------------...hhhhhhhhhhhhh.hhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.--------..---... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------BSD  PDB: A:36-88 UniProt: 158-210                   ----------------------- PROSITE
           Transcript 1 (1) 1.---------------------------------------Exon 1.3a  PDB: -      ------------------------Exon 1.5  PDB: A:24-70 UniProt: 146-192        ----------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -Exon 1.2  PDB: A:2-7 (gaps) [INCOMPLETE]----------------------Exon 1.4  PDB: A:8-23    ----------------------------------------------Exon 1.6  PDB: A:70-100 (gaps)             Transcript 1 (2)
                 1x3a A   1 G------SSGSS------------------------G-----------------------------------TNDEETIQQQILALSADKRNFLRDPPAGVQFNFDFDQMYPVALVMLQEDELLSKMRFALVPKLVKEEVFWRNYFYRVSLIKQSAQLTS--------GP---SSG 100
                            |      | 4 |       -         -      |  -         -         -         -  |     15        25        35        45        55        65        75        85        95        97   |  
                            |      2   6                        7                                   8                                                                                     95       96|  98  
                            1                                                                                                                                                                       97      

   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 1X3A)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (6, 6)

NMR Structure(hide GO term definitions)
Chain A   (SYAP1_HUMAN | Q96A49)
molecular function
    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).
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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.


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  Cis Peptide Bonds
    Val A:67 - Pro A:68   [ RasMol ]  

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