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(-) Description

Title :  SOLUTION STRUCTURE OF THE PDZ DOMAIN FROM HUMAN LIN-7 HOMOLOG B
 
Authors :  T. Suetake, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 Apr 06  (Deposition) - 14 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Lin-7B, Pdz, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Suetake, F. Hayashi, S. Yokoyama
Solution Structure Of The Pdz Domain From Human Lin-7 Homolog B
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LIN-7 HOMOLOG B
    ChainsA
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050516-07
    Expression System Vector TypePLASMID
    FragmentPDZ DOMAIN
    GeneLIN7B, MALS2, VELI2, UNQ3116/PRO10200
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymLIN-7B, HLIN7B, MAMMALIAN LIN-SEVEN PROTEIN 2, MALS-2, VERTEBRATE LIN 7 HOMOLOG 2, VELI-2 PROTEIN, HVELI2

 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 2DKR)

(-) Sites  (0, 0)

(no "Site" information available for 2DKR)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DKR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DKR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DKR)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.LIN7B_HUMAN93-175  1A:8-90

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002214591bENSE00001116427chr19:49617618-4961769881LIN7B_HUMAN1-13130--
1.2cENST000002214592cENSE00000349030chr19:49618106-49618224119LIN7B_HUMAN13-52400--
1.3bENST000002214593bENSE00000719255chr19:49618517-4961858872LIN7B_HUMAN53-76241A:1-22
1.4bENST000002214594bENSE00000719259chr19:49619520-49619729210LIN7B_HUMAN77-146701A:3-61 (gaps)64
1.5bENST000002214595bENSE00001116428chr19:49621112-49621275164LIN7B_HUMAN147-201551A:62-9029
1.6ENST000002214596ENSE00001116426chr19:49621609-49621717109LIN7B_HUMAN201-20771A:91-933

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:93
 aligned with LIN7B_HUMAN | Q9HAP6 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:143
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204   
          LIN7B_HUMAN    65 GSAEIRAHATAKATVAAFTASEGHAHPRVVELPKTDEGLGFNIMGGKEQNSPIYISRVIPGGVADRHGGLKRGDQLLSVNGVSVEGEQHEKAVELLKAAQGSVKLVVRYTPRVLEEMEARFEKMRSARRRQQHQSYSSLESRG 207
               SCOP domains d2                dkra_      A: automated matches                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..----------------.....-----eeeee.......eeee.........eeeee...hhhhhhh.......eeee..ee....hhhhhhhhhhhh..eeeeee....-----------------------------... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------PDZ  PDB: A:8-90 UniProt: 93-175                                                   -------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3b   Exon 1.4b  PDB: A:3-61 (gaps) UniProt: 77-146 [INCOMPLETE]            Exon 1.5b  PDB: A:62-90 UniProt: 147-201 [INCOMPLETE]  ------ Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------1.6     Transcript 1 (2)
                 2dkr A   1 GS----------------SGSSG-----VVELPKTDEGLGFNIMGGKEQNSPIYISRVIPGGVADRHGGLKRGDQLLSVNGVSVEGEQHEKAVELLKAAQGSVKLVVRSGP-----------------------------SSG  93
                             |       -        |4  |     |9        19        29        39        49        59        69        79        89|        -         -         -|  
                             2                3   7     8                                                                                90                            91  

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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 2DKR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DKR)

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (LIN7B_HUMAN | Q9HAP6)
molecular function
    GO:0030165    PDZ domain binding    Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
biological process
    GO:0006887    exocytosis    A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
    GO:0045199    maintenance of epithelial cell apical/basal polarity    The maintenance of the apicobasal polarity of an epithelial cell.
    GO:0007269    neurotransmitter secretion    The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium regualated exocytosis during synaptic transmission.
    GO:1903361    protein localization to basolateral plasma membrane    A process in which a protein is transported to, or maintained in, a location within a basolateral plasma membrane.
    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: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.
cellular component
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0005923    bicellular tight junction    An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.
    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:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
    GO:0098793    presynapse    The part of a synapse that is part of the presynaptic cell.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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