Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF THE FIRST PDZ DOMAIN OF HUMAN ATROPHIN-1 INTERACTING PROTEIN 1 (KIAA0705 PROTEIN)
 
Authors :  C. Zhao, T. Kigawa, N. Tochio, S. Koshiba, M. Inoue, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  20 May 03  (Deposition) - 20 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Atrophin-1 Interacting Protein 1, Pdz Domain, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Zhao, T. Kigawa, N. Tochio, S. Koshiba, M. Inoue, S. Yokoyama
Solution Structure Of The First Pdz Domain Of Human Atrophin-1 Interacting Protein 1 (Kiaa0705 Protein)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MEMBRANE ASSOCIATED GUANYLATE KINASE INVERTED-2 (MAGI-2)
    ChainsA
    EngineeredYES
    Expression System PlasmidP021030-27
    Expression System Vector TypePLASMID
    FragmentPDZ DOMAIN
    GeneKAZUSA CDNA HG03359
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymKIAA0705 PROTEIN

 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 1UEQ)

(-) Sites  (0, 0)

(no "Site" information available for 1UEQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.MAGI2_HUMAN17-101
426-495
605-668
778-860
920-1010
1147-1229
  1-
A:22-91
-
-
-
-

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003542121aENSE00001597225chr7:79082890-79082336555MAGI2_HUMAN1-1011010--
1.2ENST000003542122ENSE00001303965chr7:78636522-78636406117MAGI2_HUMAN101-140400--
1.3ENST000003542123ENSE00001685649chr7:78256555-78256436120MAGI2_HUMAN140-180410--
1.4bENST000003542124bENSE00001205406chr7:78150962-78150747216MAGI2_HUMAN180-252730--
1.6ENST000003542126ENSE00001330729chr7:78131104-78130894211MAGI2_HUMAN252-322711A:1-77
1.8ENST000003542128ENSE00000877036chr7:78119157-7811907880MAGI2_HUMAN322-349280--
1.9ENST000003542129ENSE00001145525chr7:77998530-7799847358MAGI2_HUMAN349-368200--
1.10ENST0000035421210ENSE00001145517chr7:77975360-77975239122MAGI2_HUMAN368-409420--
1.11ENST0000035421211ENSE00000698470chr7:77973277-77973095183MAGI2_HUMAN409-470621A:8-6659
1.12ENST0000035421212ENSE00001145503chr7:77885898-77885260639MAGI2_HUMAN470-6832141A:66-123 (gaps)107
1.13ENST0000035421213ENSE00001021151chr7:77830510-7783047932MAGI2_HUMAN683-693110--
1.15bENST0000035421215bENSE00001307170chr7:77824380-77824191190MAGI2_HUMAN694-757640--
1.16aENST0000035421216aENSE00001385451chr7:77814987-7781494642MAGI2_HUMAN757-771150--
1.18bENST0000035421218bENSE00001021153chr7:77807419-7780732892MAGI2_HUMAN771-801310--
1.19aENST0000035421219aENSE00001021149chr7:77797425-77797233193MAGI2_HUMAN802-866650--
1.20aENST0000035421220aENSE00001021150chr7:77789590-77789342249MAGI2_HUMAN866-949840--
1.22ENST0000035421222ENSE00001021148chr7:77764523-77764338186MAGI2_HUMAN949-1011630--
1.23ENST0000035421223ENSE00001329671chr7:77762377-77762206172MAGI2_HUMAN1011-1068580--
1.24ENST0000035421224ENSE00001308147chr7:77756733-77756514220MAGI2_HUMAN1068-1141740--
1.25ENST0000035421225ENSE00001021152chr7:77755154-77755011144MAGI2_HUMAN1142-1189480--
1.26aENST0000035421226aENSE00001021144chr7:77708402-77708264139MAGI2_HUMAN1190-1236470--
1.28bENST0000035421228bENSE00001366055chr7:77649293-776463932901MAGI2_HUMAN1236-14552200--

(-) 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:123
 aligned with MAGI2_HUMAN | Q86UL8 from UniProtKB/Swiss-Prot  Length:1455

    Alignment length:318
                                   268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568        
          MAGI2_HUMAN   259 KSAGASGEMPSQPYPAPVYSQPEELKEQMDDTKPTKPEDNEEPDPLPDNWEMAYTEKGEVYFIDHNTKTTSWLDPRLAKKAKPPEECKENELPYGWEKIDDPIYGTYYVDHINRRTQFENPVLEAKRKLQQHNMPHTELGTKPLQAPGFREKPLFTRDASQLKGTFLSTTLKKSNMGFGFTIIGGDEPDEFLQVKSVIPDGPAAQDGKMETGDVIVYINEVCVLGHTHADVVKLFQSVPIGQSVNLVLCRGYPLPFDPEDPANSMVPPLAIMERPPPVMVNGRHNYETYLEYISRTSQSVPDITDRPPHSLHSMPTDG 576
               SCOP domains d1ueqa_                                                                                                                                                   A: Membrane associated guanylate kinase inverted-2 (MAGI-2, KIAA0705)                                                                                                SCOP domains
               CATH domains 1ueqA00                                                                                                                                                   A:1-123  [code=2.30.42.10, no name defined]                                                                                                                          CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------PDZ-1ueqA01 A:22-102                                                             ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......--------------------------------------------------------------------------------------------------------------------------------------------------..........eeeeeeeee.......eeee.........eeeee....hhhh........eeeee..ee.....hhhhhhhhh......eeeeeeee.............-------------------------------------------------...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------PDZ  PDB: A:22-91 UniProt: 426-495                                    --------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: A:1-7 UniProt: 252-322 [INCOMPLETE]              ---------------------------------------------Exon 1.10  PDB: - UniProt: 368-409        ------------------------------------------------------------Exon 1.12  PDB: A:66-123 (gaps) UniProt: 470-683 [INCOMPLETE]                                               Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------Exon 1.8  PDB: -            -----------------------------------------------------------Exon 1.11  PDB: A:8-66 UniProt: 409-470 [INCOMPLETE]          ---------------------------------------------------------------------------------------------------------- Transcript 1 (2)
           Transcript 1 (3) ------------------------------------------------------------------------------------------Exon 1.9  PDB: -    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 1ueq A   1 GSSGSSG--------------------------------------------------------------------------------------------------------------------------------------------------LFTRDASQLKGTFLSTTLKKSNMGFGFTIIGGDEPDEFLQVKSVIPDGPAAQDGKMETGDVIVYINEVCVLGHTHADVVKLFQSVPIGQSVNLVLCRGYPLPFDPEDPAN-------------------------------------------------SGPSSG 123
                                  |  -         -         -         -         -         -         -         -         -         -         -         -         -         -         -   |    14        24        34        44        54        64        74        84        94       104       114  |      -         -         -         -         -  |     
                                  7                                                                                                                                                  8                                                                                                          117                                               118     

   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  (1, 1)

NMR Structure
(-)
Clan: PDZ-like (184)
(-)
Family: PDZ (172)

(-) Gene Ontology  (42, 42)

NMR Structure(hide GO term definitions)
Chain A   (MAGI2_HUMAN | Q86UL8)
molecular function
    GO:0046332    SMAD binding    Interacting selectively and non-covalently with a SMAD signaling protein.
    GO:0031697    beta-1 adrenergic receptor binding    Interacting selectively and non-covalently with a beta-1 adrenergic receptor.
    GO:0019902    phosphatase binding    Interacting selectively and non-covalently with any phosphatase.
    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:0032947    protein complex scaffold activity    A structural molecule activity that provides a physical support for the assembly of a multiprotein complex. The scaffold may or may not be part of the final complex.
    GO:0030159    receptor signaling complex scaffold activity    Functions to provide a physical support for the assembly of a multiprotein receptor signaling complex.
    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.
    GO:0070699    type II activin receptor binding    Interacting selectively and non-covalently with a type II activin receptor.
biological process
    GO:0060395    SMAD protein signal transduction    The cascade of processes by which a signal interacts with a receptor, causing a change in the activity of a SMAD protein, and ultimately effecting a change in the functioning of the cell.
    GO:1990090    cellular response to nerve growth factor stimulus    A 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 a nerve growth factor stimulus.
    GO:0072015    glomerular visceral epithelial cell development    The process whose specific outcome is the progression of a glomerular visceral epithelial cell over time, from its formation to the mature structure. A glomerular visceral epithelial cell is a specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells.
    GO:0071850    mitotic cell cycle arrest    The process in which the mitotic cell cycle is halted during one of the normal phases (G1, S, G2, M).
    GO:0032926    negative regulation of activin receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of any activin receptor signaling pathway.
    GO:0030336    negative regulation of cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0051898    negative regulation of protein kinase B signaling    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    GO:0038180    nerve growth factor signaling pathway    A series of molecular signals initiated by the binding of nerve growth factor (NGF) to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    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:0097118    neuroligin clustering involved in postsynaptic membrane assembly    The receptor clustering process involved in assembly of the postsynaptic membrane in which neuroligins are localized to distinct domains in the cell membrane. Neuroligins are neuronal cell surface proteins on the postsynaptic membrane that mediate synapse formation between neurons.
    GO:0003402    planar cell polarity pathway involved in axis elongation    The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal to modulate cytoskeletal elements and control cell polarity that contributes to axis elongation.
    GO:0010976    positive regulation of neuron projection development    Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0032516    positive regulation of phosphoprotein phosphatase activity    Any process that activates or increases the activity of a phosphoprotein phosphatase.
    GO:0002092    positive regulation of receptor internalization    Any process that activates or increases the frequency, rate or extent of receptor internalization.
    GO:2000809    positive regulation of synaptic vesicle clustering    Any process that activates or increases the frequency, rate or extent of synaptic vesicle clustering.
    GO:0051291    protein heterooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers that are not all identical. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0043113    receptor clustering    The receptor metabolic process that results in grouping of a set of receptors at a cellular location, often to amplify the sensitivity of a signaling response.
    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: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: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:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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: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: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:0036057    slit diaphragm    A specialized cell-cell junction found between the interdigitating foot processes of the glomerular epithelium (the podocytes) in the vertebrate kidney, which is adapted for facilitating glomerular filtration.
    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.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1ueq)
 
  Sites
(no "Sites" information available for 1ueq)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ueq)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1ueq
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MAGI2_HUMAN | Q86UL8
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  MAGI2_HUMAN | Q86UL8
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MAGI2_HUMAN | Q86UL81uep 1uew 1ujv 1wfv

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1UEQ)