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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SIXTH PDZ DOMAIN OF GRIP1 IN COMPLEX WITH LIPRIN C-TERMINAL PEPTIDE
 
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 :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Pdz, Grip, Liprin, 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, B
    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
 
Molecule 2 - 8-MER PEPTIDE FROM INTERACTING PROTEIN (LIPRIN)
    ChainsC, D
    EngineeredYES
    Other DetailsTHE SEQUENCE OF THIS CHEMICALLY SYNTHETIZED OCTA PEPTIDE OCCURS IN THE C-TERMIUNS OF HUMAN LIPRIN ALPHA PROTEIN
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1N7F)

(-) Sites  (0, 0)

(no "Site" information available for 1N7F)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N7F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N7F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N7F)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.GRIP1_RAT53-136
150-238
252-336
471-546
572-657
672-754
 
988-1070
  2-
-
-
-
-
A:672-753
B:672-753
-

(-) Exons   (0, 0)

(no "Exon" information available for 1N7F)

(-) 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:86
 aligned with GRIP1_RAT | P97879 from UniProtKB/Swiss-Prot  Length:1112

    Alignment length:86
                                   677       687       697       707       717       727       737       747      
           GRIP1_RAT    668 AIIYTVELKRYGGPLGITISGTEEPFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQ  753
               SCOP domains d1n7fa_ A: Glutamate receptor-interacting protein 1, GRIP1                             SCOP domains
               CATH domains 1n7fA00 A:668-753  [code=2.30.42.10, no name defined]                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......eeeee........eeeee...hhhhhhh......eeeee..ee....hhhhhhhhhh....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: A:672-753 UniProt: 672-754                                               PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                1n7f A  668 AIIYTVELKRYGGPLGITISGTEEPFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQ  753
                                   677       687       697       707       717       727       737       747      

Chain B from PDB  Type:PROTEIN  Length:86
 aligned with GRIP1_RAT | P97879 from UniProtKB/Swiss-Prot  Length:1112

    Alignment length:86
                                   677       687       697       707       717       727       737       747      
           GRIP1_RAT    668 AIIYTVELKRYGGPLGITISGTEEPFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQ  753
               SCOP domains d1n7fb_ B: Glutamate receptor-interacting protein 1, GRIP1                             SCOP domains
               CATH domains 1n7fB00 B:668-753  [code=2.30.42.10, no name defined]                                  CATH domains
           Pfam domains (1) ----PDZ-1n7fB01 B:672-751                                                           -- Pfam domains (1)
           Pfam domains (2) ----PDZ-1n7fB02 B:672-751                                                           -- Pfam domains (2)
         Sec.struct. author ..eeeeeee.......eeeee........eeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhhh..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: B:672-753 UniProt: 672-754                                               PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                1n7f B  668 AIIYTVELKRYGGPLGITISGTEEPFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQ  753
                                   677       687       697       707       717       727       737       747      

Chain C from PDB  Type:PROTEIN  Length:8
 aligned with LIPA1_HUMAN | Q13136 from UniProtKB/Swiss-Prot  Length:1202

    Alignment length:8
         LIPA1_HUMAN   1195 ATVRTYSC 1202
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ...eeee. Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                1n7f C    1 ATVRTYSC    8

Chain D from PDB  Type:PROTEIN  Length:8
 aligned with LIPA1_HUMAN | Q13136 from UniProtKB/Swiss-Prot  Length:1202

    Alignment length:8
         LIPA1_HUMAN   1195 ATVRTYSC 1202
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ...eeee. Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                1n7f D    1 ATVRTYSC    8

   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/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PDZ-like (184)
(-)
Family: PDZ (172)
1aPDZ-1n7fB01B:672-751
1bPDZ-1n7fB02B:672-751

(-) Gene Ontology  (27, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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.

Chain C,D   (LIPA1_HUMAN | Q13136)
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:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    GO:0007160    cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules.
    GO:0014047    glutamate secretion    The controlled release of glutamate by a cell. The glutamate is the most abundant excitatory neurotransmitter in the nervous system.
    GO:0090005    negative regulation of establishment of protein localization to plasma membrane    Any process that decreases the frequency, rate or extent of the directed movement of a protein to a specific location in the plasma membrane.
    GO:0051497    negative regulation of stress fiber assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of the assembly a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts.
    GO:0007269    neurotransmitter secretion    The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium regualated exocytosis during synaptic transmission.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0048786    presynaptic active zone    A specialized region of the plasma membrane and cell cortex of a presynaptic neuron; encompasses a region of the plasma membrane where synaptic vesicles dock and fuse, and a specialized cortical cytoskeletal matrix.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GRIP1_RAT | P978791m5z 1n7e 1p1d 1p1e 2qt5

(-) Related Entries Specified in the PDB File

1n7e THE SIXTH PDZ DOMAIN OF GRIP1