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(-) Description

Title :  SOLUTION STRUCTURE OF HARMONIN PDZ2 IN COMPLEX WITH THE CARBOXYL TAIL PEPTIDE OF CADHERIN23
 
Authors :  L. Pan, J. Yan, L. Wu, M. Zhang
Date :  05 Dec 08  (Deposition) - 31 Mar 09  (Release) - 21 Apr 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Protein Complex, Alternative Splicing, Coiled Coil, Deafness, Hearing, Non-Syndromic Deafness, Polymorphism, Retinitis Pigmentosa, Sensory Transduction, Usher Syndrome, Vision, Calcium, Cell Adhesion, Cell Membrane, Disease Mutation, Glycoprotein, Membrane, Phosphoprotein, Transmembrane, Structural Protein/Cell Adhesion Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Pan, J. Yan, L. Wu, M. Zhang
Assembling Stable Hair Cell Tip Link Complex Via Multidentate Interactions Between Harmonin And Cadherin 23
Proc. Natl. Acad. Sci. Usa V. 106 5575 2009
PubMed-ID: 19297620  |  Reference-DOI: 10.1073/PNAS.0901819106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HARMONIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET32A
    Expression System Vector TypeVECTOR
    FragmentPDZ2 DOMAIN, UNP RESIDUES 208-299
    GeneHARMONIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUSHER SYNDROME TYPE-1C PROTEIN, AUTOIMMUNE ENTEROPATHY-RELATED ANTIGEN AIE-75, ANTIGEN NY-CO-38/NY-CO- 37, PDZ-73 PROTEIN, RENAL CARCINOMA ANTIGEN NY-REN-3
 
Molecule 2 - OCTAMERIC PEPTIDE FROM CADHERIN-23
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET32A
    Expression System Vector TypeVECTOR
    FragmentCARBOXYL TAIL, UNP RESIDUES 3347-3354
    GeneCADHERIN23
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymOTOCADHERIN

 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 2KBS)

(-) Sites  (0, 0)

(no "Site" information available for 2KBS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.USH1C_HUMAN87-155
211-281
452-525
  1-
A:12-82
-

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003180241aENSE00001481272chr11:17565963-17565819145USH1C_HUMAN1-12120--
1.3bENST000003180243bENSE00001356343chr11:17554869-1755480268USH1C_HUMAN13-35230--
1.4bENST000003180244bENSE00000705394chr11:17553089-17552946144USH1C_HUMAN35-83490--
1.5aENST000003180245aENSE00000705392chr11:17552839-17552701139USH1C_HUMAN83-129470--
1.6ENST000003180246ENSE00000705391chr11:17548878-17548770109USH1C_HUMAN130-166370--
1.7ENST000003180247ENSE00000705390chr11:17548587-1754856325USH1C_HUMAN166-17490--
1.8ENST000003180248ENSE00000705389chr11:17548357-1754830058USH1C_HUMAN174-193200--
1.9ENST000003180249ENSE00000705388chr11:17547988-1754789495USH1C_HUMAN194-225321A:9-2618
1.10ENST0000031802410ENSE00000705386chr11:17546082-1754599885USH1C_HUMAN225-253291A:26-5429
1.11ENST0000031802411ENSE00000705385chr11:17545025-1754496660USH1C_HUMAN254-273201A:55-7420
1.12ENST0000031802412ENSE00000705384chr11:17544814-1754475857USH1C_HUMAN274-292191A:75-9319
1.13cENST0000031802413cENSE00000705383chr11:17544473-17544331143USH1C_HUMAN293-340481A:94-1007
1.14ENST0000031802414ENSE00000705382chr11:17542958-1754289366USH1C_HUMAN340-362230--
1.15aENST0000031802415aENSE00000339040chr11:17542541-17542417125USH1C_HUMAN362-404430--
1.16ENST0000031802416ENSE00000705380chr11:17539021-1753894874USH1C_HUMAN404-428250--
1.25bENST0000031802425bENSE00000705348chr11:17523527-1752348642USH1C_HUMAN429-442140--
1.26ENST0000031802426ENSE00000705285chr11:17523082-1752302954USH1C_HUMAN443-460180--
1.27bENST0000031802427bENSE00000705266chr11:17522697-17522598100USH1C_HUMAN461-494340--
1.28ENST0000031802428ENSE00000705265chr11:17519818-17519709110USH1C_HUMAN494-530370--
1.29bENST0000031802429bENSE00001386158chr11:17518360-1751830556USH1C_HUMAN531-549190--
1.31hENST0000031802431hENSE00002163620chr11:17515923-17515442482USH1C_HUMAN549-55240--

(-) 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:92
 aligned with USH1C_HUMAN | Q9Y6N9 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:92
                                   217       227       237       247       257       267       277       287       297  
         USH1C_HUMAN    208 KEKKVFISLVGSRGLGCSISSGPIQKPGIFISHVKPGSLSAEVGLEIGDQIVEVNGVDFSNLDHKEAVNVLKSSRSLTISIVAAAGRELFMT  299
               SCOP domains d2kbsa_ A: automated matches                                                                 SCOP domains
               CATH domains 2kbsA00 A:9-100  [code=2.30.42.10, no name defined]                                          CATH domains
               Pfam domains ---PDZ-2kbsA01 A:12-91                                                             --------- Pfam domains
         Sec.struct. author .eeeeee.........eeeee.......eeeeee...hhhhhhh.....eeeee..ee....hhhhhhhhhhhh..eeeeee...hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---PDZ  PDB: A:12-82 UniProt: 211-281                                     ------------------ PROSITE
           Transcript 1 (1) -----------------Exon 1.10  PDB: A:26-54      Exon 1.11           Exon 1.12          1.13c   Transcript 1 (1)
           Transcript 1 (2) Exon 1.9          -------------------------------------------------------------------------- Transcript 1 (2)
                2kbs A    9 KEKKVFISLVGSRGLGCSISSGPIQKPGIFISHVKPGSLSAEVGLEIGDQIVEVNGVDFSNLDHKEAVNVLKSSRSLTISIVAAAGRELFMT  100
                                    18        28        38        48        58        68        78        88        98  

Chain B from PDB  Type:PROTEIN  Length:8
 aligned with CAD23_HUMAN | Q9H251 from UniProtKB/Swiss-Prot  Length:3354

    Alignment length:8
         CAD23_HUMAN   3347 TPLEITEL 3354
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ....eee. Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                2kbs B  111 TPLEITEL  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)

(-) Gene Ontology  (39, 46)

NMR Structure(hide GO term definitions)
Chain A   (USH1C_HUMAN | Q9Y6N9)
molecular function
    GO:0051015    actin filament binding    Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
    GO:0032029    myosin tail binding    Interacting selectively and non-covalently with the tail region of a myosin heavy chain.
    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:0030507    spectrin binding    Interacting selectively and non-covalently with spectrin, a protein that is the major constituent of the erythrocyte cytoskeletal network. It associates with band 4.1 (see band protein) and actin to form the cytoskeletal superstructure of the erythrocyte plasma membrane. It is composed of nonhomologous chains, alpha and beta, which aggregate side-to-side in an antiparallel fashion to form dimers, tetramers, and higher polymers.
biological process
    GO:0000086    G2/M transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
    GO:1904970    brush border assembly    The aggregation, arrangement and bonding together of adjacent microvilli through the formation of Ca(2+)-dependent adhesion links between them, forming a brush border.
    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:0043623    cellular protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell.
    GO:0050957    equilibrioception    The series of events required for an organism to receive an orientational stimulus, convert it to a molecular signal, and recognize and characterize the signal. Equilibrioception refers to a combination of processes by which an organism can perceive its orientation with respect to gravity. In animals, stimuli come from labyrinth system of the inner ears, monitoring the direction of motion; visual stimuli, with information on orientation and motion; pressure receptors, which tell the organism which body surfaces are in contact with the ground; and proprioceptive cues, which report which parts of the body are in motion.
    GO:0045494    photoreceptor cell maintenance    Any process preventing the degeneration of the photoreceptor, a specialized cell type that is sensitive to light.
    GO:1904106    protein localization to microvillus    A process in which a protein is transported to, or maintained in, a location within a microvillus.
    GO:0032532    regulation of microvillus length    A process that modulates the length of a microvillus.
    GO:0050953    sensory perception of light stimulus    The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
    GO:0007605    sensory perception of sound    The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
cellular component
    GO:0045177    apical part of cell    The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
    GO:0005903    brush border    The dense covering of microvilli on the apical surface of a epithelial cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.
    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: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:0005902    microvillus    Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.
    GO:0001917    photoreceptor inner segment    The inner segment of a vertebrate photoreceptor containing mitochondria, ribosomes and membranes where opsin molecules are assembled and passed to be part of the outer segment discs.
    GO:0001750    photoreceptor outer segment    The outer segment of a vertebrate photoreceptor that contains discs of photoreceptive membranes.
    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:0032420    stereocilium    An actin-based protrusion from the apical surface of auditory and vestibular hair cells and of neuromast cells. These protrusions are supported by a bundle of cross-linked actin filaments (an actin cable), oriented such that the plus (barbed) ends are at the tip of the protrusion, capped by a tip complex which bridges to the plasma. Bundles of stereocilia act as mechanosensory organelles.
    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 B   (CAD23_HUMAN | Q9H251)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0006816    calcium ion transport    The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0016339    calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules    The attachment of one cell to another cell via adhesion molecules that require the presence of calcium for the interaction.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0050957    equilibrioception    The series of events required for an organism to receive an orientational stimulus, convert it to a molecular signal, and recognize and characterize the signal. Equilibrioception refers to a combination of processes by which an organism can perceive its orientation with respect to gravity. In animals, stimuli come from labyrinth system of the inner ears, monitoring the direction of motion; visual stimuli, with information on orientation and motion; pressure receptors, which tell the organism which body surfaces are in contact with the ground; and proprioceptive cues, which report which parts of the body are in motion.
    GO:0007156    homophilic cell adhesion via plasma membrane adhesion molecules    The attachment of a plasma membrane adhesion molecule in one cell to an identical molecule in an adjacent cell.
    GO:0060122    inner ear receptor stereocilium organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a stereocilium. A stereocilium is an actin-based protrusion from the apical surface of inner ear receptor cells.
    GO:0007626    locomotory behavior    The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
    GO:0045494    photoreceptor cell maintenance    Any process preventing the degeneration of the photoreceptor, a specialized cell type that is sensitive to light.
    GO:0051480    regulation of cytosolic calcium ion concentration    Any process involved in the maintenance of an internal steady state of calcium ions within the cytosol of a cell or between the cytosol and its surroundings.
    GO:0050896    response to stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
    GO:0050953    sensory perception of light stimulus    The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
    GO:0007605    sensory perception of sound    The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
    GO:0007601    visual perception    The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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:0032420    stereocilium    An actin-based protrusion from the apical surface of auditory and vestibular hair cells and of neuromast cells. These protrusions are supported by a bundle of cross-linked actin filaments (an actin cable), oriented such that the plus (barbed) ends are at the tip of the protrusion, capped by a tip complex which bridges to the plasma. Bundles of stereocilia act as mechanosensory organelles.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CAD23_HUMAN | Q9H2512kbr 2lsr
        USH1C_HUMAN | Q9Y6N91x5n 2kbq 2kbr 2lsr 3k1r 5f3x 5xbf

(-) Related Entries Specified in the PDB File

2kbq HARMONIN N TERMINAL DOMAIN
2kbr HARMONIN N TERMINAL DOMAIN IN COMPLEX WITH A INTERNAL PEPTIDE OF CADHERIN23