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(-) Description

Title :  SOLUTION STRUCTURE OF PDZ DOMAIN
 
Authors :  X. Li, J. Wu, Y. Shi
Date :  20 Dec 05  (Deposition) - 26 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Gopc Pdz Domain, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Li, J. Zhang, Z. Cao, J. Wu, Y. Shi
Solution Structure Of Gopc Pdz Domain And Its Interaction With The C-Terminal Motif Of Neuroligin
Protein Sci. V. 15 2149 2006
PubMed-ID: 16882988  |  Reference-DOI: 10.1110/PS.062087506
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GOLGI ASSOCIATED PDZ AND COILED-COIL MOTIF CONTAINING ISOFORM B
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET22B (+)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentPDZ DOMAIN
    GeneGOPC GENE (270-363)
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGOPC

 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 2DC2)

(-) Sites  (0, 0)

(no "Site" information available for 2DC2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DC2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DC2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DC2)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.GOPC_HUMAN288-371  1A:12-95

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003684981bENSE00001931189chr6:117923527-117923167361GOPC_HUMAN1-95950--
1.2ENST000003684982ENSE00000840039chr6:117900227-117900063165GOPC_HUMAN96-150550--
1.3ENST000003684983ENSE00001371009chr6:117898634-11789861124GOPC_HUMAN151-15880--
1.4ENST000003684984ENSE00000762781chr6:117896515-117896340176GOPC_HUMAN159-217590--
1.5aENST000003684985aENSE00000762780chr6:117894795-117894630166GOPC_HUMAN217-272560--
1.6ENST000003684986ENSE00002164938chr6:117892118-11789202396GOPC_HUMAN273-304321A:9-2820
1.7ENST000003684987ENSE00002151421chr6:117890899-117890735165GOPC_HUMAN305-359551A:29-8355
1.8ENST000003684988ENSE00002152146chr6:117888197-117888017181GOPC_HUMAN360-420611A:84-9512
1.9ENST000003684989ENSE00001017893chr6:117884547-1178814323116GOPC_HUMAN420-462430--

(-) 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:87
 aligned with GOPC_HUMAN | Q9HD26 from UniProtKB/Swiss-Prot  Length:462

    Alignment length:87
                                   294       304       314       324       334       344       354       364       
           GOPC_HUMAN   285 PIRKVLLLKEDHEGLGISITGGKEHGVPILISEIHPGQPADRCGGLHVGDAILAVNGVNLRDTKHKEAVTILSQQRGEIEFEVVYVA 371
               SCOP domains d2dc2a_ A: automated matches                                                            SCOP domains
               CATH domains 2dc2A00 A:9-95  [code=2.30.42.10, no name defined]                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........eeeeeehhhheeeeeeee...hhhhhhh.....eeeeee..ee....hhhhhhhhhhhh..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---PDZ  PDB: A:12-95 UniProt: 288-371                                                   PROSITE
               Transcript 1 Exon 1.6  PDB: A:9-2Exon 1.7  PDB: A:29-83 UniProt: 305-359                Exon 1.8     Transcript 1
                 2dc2 A   9 PIRKVLLLKEDHEGLGISITGGKEHGVPILISEIHPGQPADRCGGLHVGDAILAVNGVNLRDTKHKEAVTILSQQRGEIEFEVVYVA  95
                                    18        28        38        48        58        68        78        88       

   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
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DC2)

(-) Gene Ontology  (24, 24)

NMR Structure(hide GO term definitions)
Chain A   (GOPC_HUMAN | Q9HD26)
molecular function
    GO:0044325    ion channel binding    Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
    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).
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:0006893    Golgi to plasma membrane transport    The directed movement of substances from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane, where they fuse and release their contents by exocytosis.
    GO:0045176    apical protein localization    Any process in which a protein is transported to, or maintained in, apical regions of the cell.
    GO:0043004    cytoplasmic sequestering of CFTR protein    The selective interaction of Cystic Fibrosis Transmembrane conductance Regulator (CFTR) protein with specific molecules in the cytoplasm, thereby inhibiting its transport to the cell membrane.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    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: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:0030660    Golgi-associated vesicle membrane    The lipid bilayer surrounding a vesicle associated with the Golgi apparatus.
    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:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0005765    lysosomal membrane    The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    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.
    GO:0030140    trans-Golgi network transport vesicle    A vesicle that mediates transport between the trans-Golgi network and other parts of the cell.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GOPC_HUMAN | Q9HD262lob 4e34 4e35 4joe 4jof 4jog 4joh 4joj 4jok 4jop 4jor 4k6y 4k72 4k75 4k76 4k78 4nmo 4nmp 4nmq 4nmr 4nms 4nmt 4nmv 4q6h 4q6s

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