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(-) Description

Title :  SYNTAXIN 6
 
Authors :  K. M. S. Misura, J. B. Bock, L. C. Gonzalez, R. H. Scheller, W. I. Weis
Date :  28 May 02  (Deposition) - 17 Jul 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Snare, Three-Helix Bundle, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Misura, J. B. Bock, L. C. Gonzalez Jr. , R. H. Scheller, W. I. Weis
Three-Dimensional Structure Of The Amino-Terminal Domain Of Syntaxin 6, A Snap-25 C Homolog.
Proc. Natl. Acad. Sci. Usa V. 99 9184 2002
PubMed-ID: 12082176  |  Reference-DOI: 10.1073/PNAS.132274599
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SYNTAXIN 6
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: N-TERMINAL DOMAIN (RESIDUES 1-110)
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1LVF)

(-) Sites  (0, 0)

(no "Site" information available for 1LVF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENSRNOT000000351451aENSRNOE00000273846chr13:70121864-70122068205STX6_RAT1-12122A:4-12
B:3-12		9
10
1.2aENSRNOT000000351452aENSRNOE00000454989chr13:70136563-70136732170STX6_RAT12-69582A:12-69
B:12-69		58
58
1.3aENSRNOT000000351453aENSRNOE00000451843chr13:70139695-7013978995STX6_RAT69-100322A:69-100
B:69-100 (gaps)		32
32
1.4ENSRNOT000000351454ENSRNOE00000273878chr13:70148241-7014830363STX6_RAT101-121212A:101-109
B:101-110		9
10
1.5ENSRNOT000000351455ENSRNOE00000273873chr13:70151989-70152114126STX6_RAT122-163420--
1.6ENSRNOT000000351456ENSRNOE00000273817chr13:70153683-70153789107STX6_RAT164-199360--
1.7ENSRNOT000000351457ENSRNOE00000273167chr13:70157786-7015788095STX6_RAT199-231330--
1.9ENSRNOT000000351459ENSRNOE00000342422chr13:70167773-701693751603STX6_RAT231-255250--

(-) Sequences/Alignments

Asymmetric Unit
   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:106
 aligned with STX6_RAT | Q63635 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:106
                                    13        23        33        43        53        63        73        83        93       103      
             STX6_RAT     4 EDPFFVVKGEVQKAVNTAQGLFQRWTELLQGPSAATREEIDWTTNELRNNLRSIEWDLEDLDETISIVEANPRKFNLDATELSIRKAFITSTRQIVRDMKDQMSAS 109
               SCOP domains d1lvfa_ A: Syntaxin 6, SNAP-25 homolog                                                                     SCOP domains
               CATH domains 1lvfA00 A:4-109  [code=1.20.58.90, no name defined]                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a--------------------------------------------------------Exon 1.3a  PDB: A:69-100        Exon 1.4  Transcript 1 (1)
           Transcript 1 (2) --------Exon 1.2a  PDB: A:12-69 UniProt: 12-69                    ---------------------------------------- Transcript 1 (2)
                 1lvf A   4 EDPFFVVKGEVQKAVNTAQGLFQRWTELLQGPSAATREEIDWTTNELRNNLRSIEWDLEDLDETISIVEANPRKFNLDATELSIRKAFITSTRQIVRDMKDQMSAS 109
                                    13        23        33        43        53        63        73        83        93       103      


Chain B from PDB  Type:PROTEIN  Length:104
 aligned with STX6_RAT | Q63635 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:108
                                    12        22        32        42        52        62        72        82        92       102        
             STX6_RAT     3 MEDPFFVVKGEVQKAVNTAQGLFQRWTELLQGPSAATREEIDWTTNELRNNLRSIEWDLEDLDETISIVEANPRKFNLDATELSIRKAFITSTRQIVRDMKDQMSASS 110
               SCOP domains d1lvfb_ B: Syntaxin 6, SNAP-25 homolog                                                                       SCOP domains
               CATH domains 1lvfB00 B:3-110  [code=1.20.58.90, no name defined]                                                          CATH domains
           Pfam domains (1) --Syntaxin-6_N-1lvfB01 B:5-103                                                                       ------- Pfam domains (1)
           Pfam domains (2) --Syntaxin-6_N-1lvfB02 B:5-103                                                                       ------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........................................----..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1a --------------------------------------------------------Exon 1.3a  PDB: B:69-100 (gaps) Exon 1.4   Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.2a  PDB: B:12-69 UniProt: 12-69                    ----------------------------------------- Transcript 1 (2)
                 1lvf B   3 MEDPFFVVKGEVQKAVNTAQGLFQRWTELLQGPSAATREEIDWTTNELRNNLRSIEWDLEDLDETISIVEAN----NLDATELSIRKAFITSTRQIVRDMKDQMSASS 110
                                    12        22        32        42        52        62        72 |    | 82        92       102        
                                                                                                  74   79
   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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Syntaxin-6_N] (1)

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (STX6_RAT | Q63635)
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).
    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:0090161    Golgi ribbon formation    The formation of a continuous ribbon of interconnected Golgi stacks of flat cisternae.
    GO:0048193    Golgi vesicle transport    The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles.
    GO:0007032    endosome organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of endosomes.
    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: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:1903827    regulation of cellular protein localization    Any process that modulates the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
    GO:0032880    regulation of protein localization    Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
    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: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: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: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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0045335    phagocytic vesicle    A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis.
    GO:0043195    terminal bouton    Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.
    GO:0032588    trans-Golgi network membrane    The lipid bilayer surrounding any of the compartments that make up the trans-Golgi network.

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