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(-) Description

Title :  SOLUTION STRUCTURE OF THE SECOND CH DOMAIN OF HUMAN SPECTRIN BETA CHAIN, BRAIN 2
 
Authors :  T. Tomizawa, T. Kigawa, S. Koshiba, M. Inoue, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  15 Feb 05  (Deposition) - 15 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nppsfa, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Tomizawa, T. Kigawa, S. Koshiba, M. Inoue, S. Yokoyama
Solution Structure Of The Second Ch Domain Of Human Spectrin Beta Chain, Brain 2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SPECTRIN BETA CHAIN, BRAIN 2
    ChainsA
    EngineeredYES
    Expression System PlasmidP040705-11
    Expression System Vector TypePLASMID
    FragmentCH DOMAIN
    GeneSPTBN2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymSPECTRIN, NON-ERYTHROID BETA CHAIN 2, BETA-III SPECTRIN

 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 1WYQ)

(-) Sites  (0, 0)

(no "Site" information available for 1WYQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_026767L253PSPTN2_HUMANDisease (SCA5)121918306AL83P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHPS50021 Calponin homology domain profile.SPTN2_HUMAN57-161
176-278
  1-
A:8-108

(-) Exons   (6, 6)

NMR Structure (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003099962bENSE00001367680chr11:66488870-6648882150SPTN2_HUMAN-00--
1.3aENST000003099963aENSE00001188149chr11:66488733-66488555179SPTN2_HUMAN1-53530--
1.4ENST000003099964ENSE00001188138chr11:66483452-66483301152SPTN2_HUMAN53-103510--
1.5bENST000003099965bENSE00001757789chr11:66482866-66482693174SPTN2_HUMAN104-161581A:1-6 (gaps)10
1.6ENST000003099966ENSE00001604316chr11:66481878-6648178792SPTN2_HUMAN162-192311A:7-2216
1.7ENST000003099967ENSE00001188110chr11:66481642-6648156281SPTN2_HUMAN192-219281A:22-4928
1.8ENST000003099968ENSE00001188096chr11:66481217-66481102116SPTN2_HUMAN219-258401A:49-8840
1.9ENST000003099969ENSE00001592767chr11:66478500-66478388113SPTN2_HUMAN258-295381A:88-12134
1.10ENST0000030999610ENSE00001188080chr11:66478240-66478053188SPTN2_HUMAN296-358631A:122-1276
1.11ENST0000030999611ENSE00001188071chr11:66476490-66476373118SPTN2_HUMAN358-397400--
1.12ENST0000030999612ENSE00001188065chr11:66475770-66475612159SPTN2_HUMAN398-450530--
1.13ENST0000030999613ENSE00001188053chr11:66475289-66474987303SPTN2_HUMAN451-5511010--
1.14ENST0000030999614ENSE00001188049chr11:66473308-66473155154SPTN2_HUMAN552-603520--
1.15bENST0000030999615bENSE00001188040chr11:66472939-66472069871SPTN2_HUMAN603-8932910--
1.16ENST0000030999616ENSE00001188033chr11:66469192-66469055138SPTN2_HUMAN893-939470--
1.17ENST0000030999617ENSE00001188026chr11:66468753-66467997757SPTN2_HUMAN939-11912530--
1.18ENST0000030999618ENSE00001188017chr11:66467079-66466877203SPTN2_HUMAN1192-1259680--
1.19ENST0000030999619ENSE00001188009chr11:66466553-6646646391SPTN2_HUMAN1259-1289310--
1.20bENST0000030999620bENSE00001750551chr11:66466256-66466110147SPTN2_HUMAN1290-1338490--
1.21ENST0000030999621ENSE00001187985chr11:66464011-66463748264SPTN2_HUMAN1339-1426880--
1.22bENST0000030999622bENSE00001187979chr11:66461834-66461610225SPTN2_HUMAN1427-1501750--
1.23ENST0000030999623ENSE00001187965chr11:66461332-6646124390SPTN2_HUMAN1502-1531300--
1.24ENST0000030999624ENSE00001187956chr11:66460917-66460657261SPTN2_HUMAN1532-1618870--
1.25ENST0000030999625ENSE00001187950chr11:66460571-66460441131SPTN2_HUMAN1619-1662440--
1.26ENST0000030999626ENSE00001187940chr11:66460211-66460007205SPTN2_HUMAN1662-1730690--
1.27ENST0000030999627ENSE00001187935chr11:66459129-66458755375SPTN2_HUMAN1731-18551250--
1.28bENST0000030999628bENSE00001187927chr11:66457754-66457510245SPTN2_HUMAN1856-1937820--
1.29ENST0000030999629ENSE00001187921chr11:66457414-66457276139SPTN2_HUMAN1937-1983470--
1.31ENST0000030999631ENSE00001187911chr11:66456651-6645656785SPTN2_HUMAN1984-2012290--
1.32cENST0000030999632cENSE00001187901chr11:66456320-66456124197SPTN2_HUMAN2012-2077660--
1.33ENST0000030999633ENSE00001187897chr11:66455782-66455640143SPTN2_HUMAN2078-2125480--
1.34ENST0000030999634ENSE00001187890chr11:66455550-6645547576SPTN2_HUMAN2125-2150260--
1.35ENST0000030999635ENSE00001187882chr11:66455389-6645533951SPTN2_HUMAN2151-2167170--
1.36bENST0000030999636bENSE00001187875chr11:66455118-66454898221SPTN2_HUMAN2168-2241740--
1.37aENST0000030999637aENSE00001187869chr11:66454638-66454465174SPTN2_HUMAN2241-2299590--
1.38bENST0000030999638bENSE00001187863chr11:66453911-6645386943SPTN2_HUMAN2299-2313150--
1.38eENST0000030999638eENSE00001226024chr11:66453575-66452721855SPTN2_HUMAN2314-2390770--

(-) 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:127
 aligned with SPTN2_HUMAN | O15020 from UniProtKB/Swiss-Prot  Length:2390

    Alignment length:203
                                   146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336   
          SPTN2_HUMAN   137 GSHDIVDGNHRLTLGLVWTIILRFQIQDISVETEDNKEKKSAKDALLLWCQMKTAGYPNVNVHNFTTSWRDGLAFNAIVHKHRPDLLDFESLKKCNAHYNLQNAFNLAEKELGLTKLLDPEDVNVDQPDEKSIITYVATYYHYFSKMKALAVEGKRIGKVLDHAMEAERLVEKYESLASELLQWIEQTIVTLNDRQLANSLSG 339
               SCOP domains d1    wyqa                              _ A: automated matches                                                                                                                                              SCOP domains
               CATH domains -----------------------------------------1wyqA01 A:8-112 Actin-binding Protein, T-fimbrin; domain 1                                               --------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..----....------------------------------..hhhhhhhhhhhhhh...............hhhhhhhhhhhh.............hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh........------------------------------------------...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------P-------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CH  PDB: -               --------------CH  PDB: A:8-108 UniProt: 176-278                                                                      ------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5b [INCOMPLETE]   Exon 1.6  PDB: A:7-22          --------------------------Exon 1.8  PDB: A:49-88 UniProt: 219-258 -------------------------------------Exon 1.10  PDB: A:122-127 UniProt: 296-358   Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------Exon 1.7  PDB: A:22-49      --------------------------------------Exon 1.9  PDB: A:88-121 [INCOMPLETE]  -------------------------------------------- Transcript 1 (2)
                 1wyq A   1 GS----SGSS------------------------------GAKDALLLWCQMKTAGYPNVNVHNFTTSWRDGLAFNAIVHKHRPDLLDFESLKKCNAHYNLQNAFNLAEKELGLTKLLDPEDVNVDQPDEKSIITYVATYYHYFSKMKALAVEGK------------------------------------------SGPSSG 127
                             |    |  6         -         -         -|       16        26        36        46        56        66        76        86        96       106       116    |    -         -         -         -       124   
                             2    3  6                              7                                                                                                               121                                        122     

   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  (1, 1)

NMR Structure

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

NMR Structure(hide GO term definitions)
Chain A   (SPTN2_HUMAN | O15020)
molecular function
    GO:0005088    Ras guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    GO:0005200    structural constituent of cytoskeleton    The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
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:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0051693    actin filament capping    The binding of a protein or protein complex to the end of an actin filament, thus preventing the addition, exchange or removal of further actin subunits.
    GO:0030534    adult behavior    Behavior in a fully developed and mature organism.
    GO:0019886    antigen processing and presentation of exogenous peptide antigen via MHC class II    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0071361    cellular response to ethanol    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
    GO:0021692    cerebellar Purkinje cell layer morphogenesis    The process in which the anatomical structure of the cerebellar Purkinje cell layer is generated and organized. The Purkinje cell layer lies just underneath the molecular layer of the cerebellar cortex. It contains the neuronal cell bodies of the Purkinje cells that are arranged side by side in a single layer. Candelabrum interneurons are vertically oriented between the Purkinje cells. Purkinje neurons are inhibitory and provide the output of the cerebellar cortex through axons that project into the white matter. Extensive dendritic trees from the Purkinje cells extend upward in a single plane into the molecular layer where they synapse with parallel fibers of granule cells.
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0007416    synapse assembly    The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional).
    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:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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: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:0008091    spectrin    Membrane associated dimeric protein (240 and 220 kDa) of erythrocytes. Forms a complex with ankyrin, actin and probably other components of the membrane cytoskeleton, so that there is a mesh of proteins underlying the plasma membrane, potentially restricting the lateral mobility of integral proteins.
    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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SPTN2_HUMAN | O150201wjm

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