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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SIXTH PDZ DOMAIN OF GRIP1
 
Authors :  Y. J. Im, S. H. Park, S. H. Rho, J. H. Lee, G. B. Kang, M. Sheng, E. Kim, S. H. Eom
Date :  14 Nov 02  (Deposition) - 12 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Pdz, Grip, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. J. Im, S. H. Park, S. H. Rho, J. H. Lee, G. B. Kang, M. Sheng, E. Kim, S. H. Eom
Crystal Structure Of Grip1 Pdz6-Peptide Complex Reveals The Structural Basis For Class Ii Pdz Target Recognition And Pdz Domain-Mediated Multimerization
J. Biol. Chem. V. 278 8501 2003
PubMed-ID: 12493751  |  Reference-DOI: 10.1074/JBC.M212263200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMPA RECEPTOR INTERACTING PROTEIN GRIP
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-4T
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentSIXTH PDZ DOMAIN
    GeneGRIP1
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymGLUTAMATE RECEPTOR INTERACTING PROTEIN 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1N7E)

(-) Sites  (0, 0)

(no "Site" information available for 1N7E)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N7E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N7E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N7E)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.GRIP1_RAT53-136
150-238
252-336
471-546
572-657
672-754
988-1070
  1-
-
-
-
-
A:672-754
-

(-) Exons   (0, 0)

(no "Exon" information available for 1N7E)

(-) Sequences/Alignments

Asymmetric/Biological 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:95
 aligned with GRIP1_RAT | P97879 from UniProtKB/Swiss-Prot  Length:1112

    Alignment length:95
                                   676       686       696       706       716       726       736       746       756     
            GRIP1_RAT   667 GAIIYTVELKRYGGPLGITISGTEEPFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQTDAQPASS 761
               SCOP domains d1n7ea_ A: Glutamate receptor-interacting protein 1, GRIP1                                      SCOP domains
               CATH domains 1n7eA00 A:667-761  [code=2.30.42.10, no name defined]                                           CATH domains
               Pfam domains -----PDZ-1n7eA01 A:672-751                                                           ---------- Pfam domains
         Sec.struct. author ...eeeeeee.......eeee.........eeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhh...eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PDZ  PDB: A:672-754 UniProt: 672-754                                               ------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 1n7e A 667 GAIIYTVELKRYGGPLGITISGTEEPFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQTDAQPASS 761
                                   676       686       696       706       716       726       736       746       756     

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PDZ-like (184)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GRIP1_RAT | P97879)
molecular function
    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:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0030159    receptor signaling complex scaffold activity    Functions to provide a physical support for the assembly of a multiprotein receptor signaling complex.
biological process
    GO:0016358    dendrite development    The process whose specific outcome is the progression of the dendrite over time, from its formation to the mature structure. A dendrite is a freely branching protoplasmic process of a nerve cell.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    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.
cellular component
    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: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:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        GRIP1_RAT | P978791m5z 1n7f 1p1d 1p1e 2qt5

(-) Related Entries Specified in the PDB File

1n7f THE SIXTH PDZ DOMAIN OF GRIP1 IN COMPLEX WITH LIPRIN C- TERMINAL PEPTIDE