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(-) Description

Title :  VAM3P N-TERMINAL DOMAIN SOLUTION STRUCTURE
 
Authors :  I. Dulubova, T. Yamaguchi, Y. Wang, T. C. Sudhof, J. Rizo
Date :  24 Dec 00  (Deposition) - 07 Mar 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Up-And-Down Three-Helix Bundle Insertion Preceding Proline In An Alpha-Helix, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. Dulubova, T. Yamaguchi, Y. Wang, T. C. Sudhof, J. Rizo
Vam3P Structure Reveals Conserved And Divergent Properties Of Syntaxins.
Nat. Struct. Biol. V. 8 258 2001
PubMed-ID: 11224573  |  Reference-DOI: 10.1038/85012
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SYNTAXIN VAM3
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-KT
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 23-119
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 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 1HS7)

(-) Sites  (0, 0)

(no "Site" information available for 1HS7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HS7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HS7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HS7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1HS7)

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YOR106W1YOR106W.1XV:519122-519973852VAM3_YEAST1-2832831A:23-11997

(-) 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:97
 aligned with VAM3_YEAST | Q12241 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:97
                                    32        42        52        62        72        82        92       102       112       
           VAM3_YEAST    23 TNQKTKELSNLIETFAEQSRVLEKECTKIGSKRDSKELRYKIETELIPNCTSVRDKIESNILIHQNGKLSADFKNLKTKYQSLQQSYNQRKSLFPLK 119
               SCOP domains d1hs7a_ A: Vam3p N-terminal domain                                                                SCOP domains
               CATH domains 1hs7A00 A:23-119  [code=1.20.58.70, no name defined]                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:23-119 UniProt: 1-283 [INCOMPLETE]                                               Transcript 1
                 1hs7 A  23 TNQKTKELSNLIETFAEQSRVLEKECTKIGSKRDSKELRYKIETELIPNCTSVRDKIESNILIHQNGKLSADFKNLKTKYQSLQQSYNQRKSLFPLK 119
                                    32        42        52        62        72        82        92       102       112       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HS7)

(-) Gene Ontology  (20, 20)

NMR Structure(hide GO term definitions)
Chain A   (VAM3_YEAST | Q12241)
molecular function
    GO:0005484    SNAP receptor activity    Acting as a marker to identify a membrane and interacting selectively with one or more SNAREs on another membrane to mediate membrane fusion.
    GO:0000149    SNARE binding    Interacting selectively and non-covalently with a SNARE (soluble N-ethylmaleimide-sensitive factor attached protein receptor) protein.
    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).
biological process
    GO:0006896    Golgi to vacuole transport    The directed movement of substances from the Golgi to the vacuole.
    GO:0097352    autophagosome maturation    Removal of PI3P and Atg8/LC3 after the closure of the phagophore and before the fusion with the endosome/lysosome (e.g. mammals and insects) or vacuole (yeast), and that very likely destabilizes other Atg proteins and thus enables their efficient dissociation and recycling.
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    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:0034727    piecemeal microautophagy of nucleus    Degradation of a cell nucleus by lysosomal microautophagy.
    GO:0042144    vacuole fusion, non-autophagic    The fusion of two vacuole membranes to form a single vacuole.
    GO:0048278    vesicle docking    The initial attachment of a transport vesicle membrane to the target membrane, mediated by proteins protruding from the membrane of the vesicle and the target membrane. Docking requires only that the two membranes come close enough for these proteins to interact and adhere.
    GO:0006906    vesicle fusion    Fusion of the membrane of a transport vesicle with its target membrane.
    GO:0051469    vesicle fusion with vacuole    The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the vacuole.
    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:0031201    SNARE complex    A protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers. One well-characterized example is the neuronal SNARE complex formed of synaptobrevin 2, syntaxin 1a, and SNAP-25.
    GO:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    GO:0000329    fungal-type vacuole membrane    The lipid bilayer surrounding a vacuole, the shape of which correlates with cell cycle phase. The membrane separates its contents from the cytoplasm of the cell. An example of this structure is found in Saccharomyces cerevisiae.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005774    vacuolar membrane    The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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