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(-) Description

Title :  SH3 DOMAIN OF HUMAN NEPHROCYSTIN
 
Authors :  A. Le Maire, T. Weber, S. Saunier, C. Antignac, A. Ducruix, F. Dardel
Date :  07 Jan 04  (Deposition) - 18 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (17x)
Keywords :  Beta Barrel, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Le Maire, T. Weber, S. Saunier, I. Broutin, C. Antignac, A. Ducruix, F. Dardel
Solution Nmr Structure Of The Sh3 Domain Of Human Nephrocystin And Analysis Of A Mutation-Causing Juvenile Nephronophthisis.
Proteins V. 59 347 2005
PubMed-ID: 15723349  |  Reference-DOI: 10.1002/PROT.20344
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEPHROCYSTIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-4T-2
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentSH3 DOMAIN
    GeneNPHP1, NPH1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymJUVENILE NEPHRONOPHTHISIS 1 PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (17x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1S1N)

(-) Sites  (0, 0)

(no "Site" information available for 1S1N)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S1N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S1N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S1N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S1N)

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003932721aENSE00001829659chr2:110962643-110962477167NPHP1_HUMAN1-23230--
1.3ENST000003932723ENSE00001636509chr2:110959071-11095899874NPHP1_HUMAN24-48250--
1.4ENST000003932724ENSE00001772412chr2:110937261-11093720161NPHP1_HUMAN48-68210--
1.6aENST000003932726aENSE00000963506chr2:110936124-110936000125NPHP1_HUMAN69-110420--
1.7ENST000003932727ENSE00001255671chr2:110927575-110927383193NPHP1_HUMAN110-174651A:153-17422
1.8ENST000003932728ENSE00000963508chr2:110926130-110926029102NPHP1_HUMAN175-208341A:175-20834
1.9ENST000003932729ENSE00001255651chr2:110922732-110922629104NPHP1_HUMAN209-243351A:209-2124
1.10bENST0000039327210bENSE00001255706chr2:110922307-110922097211NPHP1_HUMAN243-313710--
1.10eENST0000039327210eENSE00001009341chr2:110920709-11092062585NPHP1_HUMAN314-342290--
1.11ENST0000039327211ENSE00000963512chr2:110919274-11091918095NPHP1_HUMAN342-373320--
1.12ENST0000039327212ENSE00000963513chr2:110917832-110917704129NPHP1_HUMAN374-416430--
1.13ENST0000039327213ENSE00000963514chr2:110907833-11090775975NPHP1_HUMAN417-441250--
1.14ENST0000039327214ENSE00000963515chr2:110905603-110905493111NPHP1_HUMAN442-478370--
1.15ENST0000039327215ENSE00000963516chr2:110904412-11090433083NPHP1_HUMAN479-506280--
1.16aENST0000039327216aENSE00000963517chr2:110902146-11090207077NPHP1_HUMAN506-532270--
1.16dENST0000039327216dENSE00000963518chr2:110901218-110901119100NPHP1_HUMAN532-565340--
1.17ENST0000039327217ENSE00001255563chr2:110889368-110889256113NPHP1_HUMAN565-603390--
1.18aENST0000039327218aENSE00001255552chr2:110886836-11088676374NPHP1_HUMAN603-627250--
1.18dENST0000039327218dENSE00001255543chr2:110883258-11088321445NPHP1_HUMAN628-642150--
1.18iENST0000039327218iENSE00001932854chr2:110881640-110880913728NPHP1_HUMAN643-732900--

(-) 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:60
 aligned with NPHP1_HUMAN | O15259 from UniProtKB/Swiss-Prot  Length:732

    Alignment length:60
                                   162       172       182       192       202       212
          NPHP1_HUMAN   153 TGEEYIAVGDFTAQQVGDLTFKKGEILLVIEKKPDGWWIAKDAKGNEGLVPRTYLEPYSE 212
               SCOP domains d1s1na_ A: automated matches                                 SCOP domains
               CATH domains 1s1nA00 A:153-212 SH3 Domains                                CATH domains
               Pfam domains -----SH3_1-1s1nA01 A:158-204                        -------- Pfam domains
         Sec.struct. author ..eeeee.................eeeee.......eeeee.....eeeee...eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.7 [INCOMPLETE] Exon 1.8  PDB: A:175-208          1.9  Transcript 1
                 1s1n A 153 TGEEYIAVGDFTAQQVGDLTFKKGEILLVIEKKPDGWWIAKDAKGNEGLVPRTYLEPYSE 212
                                   162       172       182       192       202       212

   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: SH3 (175)

(-) Gene Ontology  (24, 24)

NMR Structure(hide GO term definitions)
Chain A   (NPHP1_HUMAN | O15259)
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:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0030030    cell projection organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0007588    excretion    The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds.
    GO:0060041    retina development in camera-type eye    The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
    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.
    GO:0016337    single organismal cell-cell adhesion    The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
    GO:0048515    spermatid differentiation    The process whose specific outcome is the progression of a spermatid over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0007632    visual behavior    The behavior of an organism in response to a visual stimulus.
cellular component
    GO:0005912    adherens junction    A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
    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:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    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:0005929    cilium    A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031514    motile cilium    A cilium which may have a variable arrangement of axonemal microtubules and also contains molecular motors. It may beat with a whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface, such as on epithelial cells that line the lumenal ducts of various tissues; or they may display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface to affect asymmetric body plan organization. Motile cilia can be found in single as well as multiple copies per cell.
    GO:0032391    photoreceptor connecting cilium    The portion of the photoreceptor cell cilium linking the photoreceptor inner and outer segments. It's considered to be equivalent to the ciliary transition zone.

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