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(-) Description

Title :  SOLUTION STRUCTURE OF RSGI RUH-009, AN N-TERMINAL DOMAIN OF VTI1A [MUS MUSCULUS]
 
Authors :  T. Abe, H. Hirota, T. Tomizawa, S. Koshiba, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  10 Mar 04  (Deposition) - 03 May 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Snare, Habc Domain, Vti1, Up And Down Three Helix Bundle, Left-Handed Twist, Vesicle Transport, Membrane Fusion, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Abe, H. Hirota, T. Tomizawa, S. Koshiba, T. Kigawa, S. Yokoyama
Solution Structure Of Rsgi Ruh-009, An N-Terminal Domain Of Vti1A [Mus Musculus]
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VESICLE TRANSPORT THROUGH INTERACTION WITH T- SNARES HOMOLOG 1A
    ChainsA
    EngineeredYES
    Expression System PlasmidP030825-55
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DOMAIN (RESIDUES 6-94)
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsCELL-FREE PROTEIN SYNTHESIS SYSTEM
    SynonymVESICLE TRANSPORT V-SNARE PROTEIN VTI1-LIKE 2, VTI1-RP2

 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 1VCS)

(-) Sites  (0, 0)

(no "Site" information available for 1VCS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VCS)

(-) 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:102
 aligned with VTI1A_MOUSE | O89116 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:114
                              1                                                                                                               
                              |      8        18        28        38        48        58        68        78        88        98       108    
          VTI1A_MOUSE     - --MSSDFEGYEQDFAVLTAEITSKIARVPRLPPDEKKQMVANVEKQLEEARELLEQMDLEVREIPPQSRGMYSNRMRSYKQEMGKLETDFKRSRIAYSDEVRNELLGDAGNSSE 112
               SCOP domains -------d1vcsa1 A:8-96 Vesicle transport v-SNARE protein Vti1-like 2                             ------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------V-SNARE-1vcsA01 A:14-92                                                        ---------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhh.hh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh..------------..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1vcs A   1 GSSGSSGEGYEQDFAVLTAEITSKIARVPRLPPDEKKQMVANVEKQLEEARELLEQMDLEVREIPPQSRGMYSNRMRSYKQEMGKLETDFKRSRIAS------------GPSSG 102
                                    10        20        30        40        50        60        70        80        90      |  -        98    
                                                                                                                           97           98    

   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  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (31, 31)

NMR Structure(hide GO term definitions)
Chain A   (VTI1A_MOUSE | O89116)
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.
biological process
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0090161    Golgi ribbon formation    The formation of a continuous ribbon of interconnected Golgi stacks of flat cisternae.
    GO:0006896    Golgi to vacuole transport    The directed movement of substances from the Golgi to the vacuole.
    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:0006891    intra-Golgi vesicle-mediated transport    The directed movement of substances within the Golgi, mediated by small transport vesicles. These either fuse with the cis-Golgi or with each other to form the membrane stacks known as the cis-Golgi reticulum (network).
    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:0006623    protein targeting to vacuole    The process of directing proteins towards the vacuole, usually using signals contained within the protein.
    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:0042147    retrograde transport, endosome to Golgi    The directed movement of membrane-bounded vesicles from endosomes back to the trans-Golgi network where they are recycled for further rounds of transport.
    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.
    GO:0048280    vesicle fusion with Golgi apparatus    The joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane around the Golgi.
    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.
    GO:0050882    voluntary musculoskeletal movement    The movement of an organism or part of an organism using mechanoreceptors, the nervous system, striated muscle and/or the skeletal system that can be controlled at will.
cellular component
    GO:0012507    ER to Golgi transport vesicle membrane    The lipid bilayer surrounding a vesicle transporting substances from the endoplasmic reticulum to the Golgi.
    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:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    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:0005776    autophagosome    A double-membrane-bounded compartment that engulfs endogenous cellular material as well as invading microorganisms to target them to the vacuole/lysosome for degradation as part of macroautophagy.
    GO:0030136    clathrin-coated vesicle    A vesicle with a coat formed of clathrin connected to the membrane via one of the clathrin adaptor complexes.
    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:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    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:0031902    late endosome membrane    The lipid bilayer surrounding a late endosome.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0044306    neuron projection terminus    The specialized, terminal region of a neuron projection such as an axon or a dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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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