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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2 (ALL CATION BINDING SITES OCCUPIED BY CALCIUM)
 
Authors :  M. Sotomayor, W. Weihofen, R. Gaudet, D. P. Corey
Date :  07 May 09  (Deposition) - 21 Apr 10  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.36
Chains :  Asym./Biol. Unit :  A
Keywords :  Cell Adhesion, Hearing, Deafness (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Sotomayor, W. Weihofen, R. Gaudet, D. P. Corey
Structural Determinants Of Cadherin-23 Function In Hearing And Deafness.
Neuron V. 66 85 2010
PubMed-ID: 20399731  |  Reference-DOI: 10.1016/J.NEURON.2010.03.028

(-) Compounds

Molecule 1 - CADHERIN-23
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET21A
    Expression System Vector TypePLASMID
    FragmentEC1-2, RESIDUES 24-228
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymOTOCADHERIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4K4Ligand/IonPOTASSIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:4 , ARG A:5 , ASP A:37 , ASP A:39 , ASP A:41 , ASP A:87BINDING SITE FOR RESIDUE CA A 401
02AC2SOFTWAREGLU A:22 , ASP A:72 , GLU A:74 , ASP A:105 , HOH A:2123 , HOH A:2126BINDING SITE FOR RESIDUE CA A 402
03AC3SOFTWAREGLU A:22 , GLU A:74 , ASP A:102 , VAL A:103 , ASP A:105 , ASP A:138BINDING SITE FOR RESIDUE CA A 403
04AC4SOFTWAREASN A:104 , ASN A:106 , ASP A:136 , ASP A:138 , GLY A:142 , ASP A:187BINDING SITE FOR RESIDUE CA A 404
05AC5SOFTWAREVAL A:47 , HOH A:2022 , HOH A:2023 , HOH A:2024 , HOH A:2068 , HOH A:2069 , HOH A:2078BINDING SITE FOR RESIDUE K A 501
06AC6SOFTWAREASN A:133 , HOH A:2067 , HOH A:2146 , HOH A:2149 , HOH A:2158 , HOH A:2168BINDING SITE FOR RESIDUE K A 502
07AC7SOFTWAREGLU A:121 , GLU A:174 , ASP A:206 , GLU A:208 , HOH A:2171 , HOH A:2172BINDING SITE FOR RESIDUE K A 503
08AC8SOFTWAREASP A:136 , GLY A:143 , HOH A:2152 , HOH A:2153BINDING SITE FOR RESIDUE K A 601
09AC9SOFTWAREPHE A:9 , ILE A:92 , ARG A:94 , ASN A:122 , HOH A:2139BINDING SITE FOR RESIDUE CL A 701
10BC1SOFTWAREASP A:102 , ASN A:104 , LEU A:139 , ALA A:141 , GLY A:142 , ASP A:189 , LYS A:190BINDING SITE FOR RESIDUE GOL A 1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:113 -Pro A:114
2Gln A:150 -Pro A:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CAD23_MOUSE_002 *M229VCAD23_MOUSE  ---  ---AL207V
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CADHERIN_2PS50268 Cadherins domain profile.CAD23_MOUSE42-132
133-236
237-348
349-460
461-561
562-671
672-784
779-890
891-995
996-1102
1103-1208
1210-1313
1314-1418
1420-1527
1529-1634
1635-1744
1759-1851
1852-1959
1960-2069
2070-2174
2175-2293
2297-2402
2403-2509
2510-2611
2614-2722
2729-2846
2847-2975
  2A:20-110
A:111-206
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
2CADHERIN_1PS00232 Cadherin domain signature.CAD23_MOUSE120-130
336-346
549-559
659-669
766-776
878-888
1090-1100
1406-1416
1515-1525
1622-1632
1732-1742
1839-1849
1947-1957
2057-2067
2281-2291
2390-2400
2599-2609
  1A:98-108
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 2WHV)

(-) 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:208
 aligned with CAD23_MOUSE | Q99PF4 from UniProtKB/Swiss-Prot  Length:3354

    Alignment length:208
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222        
          CAD23_MOUSE    23 GQVNRLPFFTNHFFDTYLLISEDTPVGSSVTQLLARDMDNDPLVFGVSGEEASRFFAVEPDTGVVWLRQPLDRETKSEFTVEFSVSDHQGVITRKVNIQVGDVNDNAPTFHNQPYSVRIPENTPVGTPIFIVNATDPDLGAGGSVLYSFQPPSPFFAIDSARGIVTVIQELDYEVTQAYQLTVNATDQDKTRPLSTLANLAIIITDMQ 230
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------Cadherin-2whvA01 A:115-205                                                                 --- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------Cadherin-2whvA02 A:115-205                                                                 --- Pfam domains (2)
         Sec.struct. author .......ee.hhhhhh.eeee.......eeee..ee.......eeeeehhhhhhheee.....eeee..........eeeeeeeee....eeeeeeeeeee.......ee....eeeeee.......eeee..ee...hhhhh.eeeee......eee.....eeee..........eeeeeeeeee.......eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V- SAPs(SNPs)
                PROSITE (1) -------------------CADHERIN_2  PDB: A:20-110 UniProt: 42-132                                                  CADHERIN_2  PDB: A:111-206 UniProt: 133-236                                                        PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------CADHERIN_1 ---------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2whv A   1 MQVNRLPFFTNHFFDTYLLISEDTPVGSSVTQLLARDMDNDPLVFGVSGEEASRFFAVEPDTGVVWLRQPLDRETKSEFTVEFSVSDHQGVITRKVNIQVGDVNDNAPTFHNQPYSVRIPENTPVGTPIFIVNATDPDLGAGGSVLYSFQPPSPFFAIDSARGIVTVIQELDYEVTQAYQLTVNATDQDKTRPLSTLANLAIIITDLE 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        

   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  (0, 0)

(no "SCOP Domain" information available for 2WHV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WHV)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: E-set (290)

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CAD23_MOUSE | Q99PF4)
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:0042491    auditory receptor cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of an auditory hair cell.
    GO:0060088    auditory receptor cell 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 auditory hair cells.
    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:0048839    inner ear development    The process whose specific outcome is the progression of the inner ear over time, from its formation to the mature structure.
    GO:0042472    inner ear morphogenesis    The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively.
    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:0048563    post-embryonic animal organ morphogenesis    Morphogenesis, during the post-embryonic phase, of an animal tissue or tissues that work together to perform a specific function or functions. Morphogenesis pertains to process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    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: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:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    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:0060091    kinocilium    A nonmotile primary cilium that is found at the apical surface of auditory receptor cells. The kinocilium is surrounded by actin-based stereocilia.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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: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:0032426    stereocilium tip    A distinct compartment at the tip of a stereocilium, distal to the site of attachment to the apical cell surface. It consists of a dense matrix bridging the barbed ends of the stereocilium actin filaments with the overlying plasma membrane, is dynamic compared to the shaft, and is required for stereocilium elongation.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CAD23_MOUSE | Q99PF42wbx 2wcp 2wd0 3mvs 4apx 4aq8 4aqa 4aqe 4axw 4xxw

(-) Related Entries Specified in the PDB File

2wbx CRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1
2wcp CRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2
2wd0 CRYSTAL STRUCTURE OF NONSYNDROMIC DEAFNESS (DFNB12) ASSOCIATED MUTANT D124G OF MOUSE CADHERIN-23 EC1-2