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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2 AND PROTOCADHERIN-15 EC1-2 SPLICE VARIANT
 
Authors :  Y. Narui, M. Sotomayor
Date :  31 Jan 15  (Deposition) - 04 May 16  (Release) - 04 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B,C  (1x)
Biol. Unit 2:  A,D  (1x)
Keywords :  Mechanotransduction, Calcium Binding Protein, Cell Adhesion, Hearing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Narui, M. Sotomayor
Crystal Structure Of Mouse Cadherin-23 Ec1-2 And Protocadherin-15 Ec1-2 Splice Variant
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTOCADHERIN-15
    Chains: B, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PCDH15
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - CADHERIN-23
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CDH23
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: OTOCADHERIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):  BC 
Biological Unit 2 (1x): A  D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
1CA14Ligand/IonCALCIUM ION
2CL2Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU B:27 , GLU B:28 , ASP B:83 , ASP B:85 , ASP B:121 , HOH B:1224binding site for residue CA B 1001
02AC2SOFTWAREGLU B:27 , ASP B:85 , ASP B:118 , ARG B:119 , ASP B:121 , ASP B:159binding site for residue CA B 1002
03AC3SOFTWAREASN B:120 , ASN B:122 , ASP B:157 , ASP B:159 , ASN B:163 , ASP B:215binding site for residue CA B 1003
04AC4SOFTWAREPRO B:19 , ALA B:20 , ASP C:101 , HOH C:1223binding site for residue CL B 1004
05AC5SOFTWAREGLU A:27 , GLU A:28 , ASP A:83 , ASP A:85 , ASP A:121 , HOH A:1164binding site for residue CA A 1001
06AC6SOFTWAREGLU A:27 , ASP A:85 , ASP A:118 , ARG A:119 , ASP A:121 , ASP A:159binding site for residue CA A 1002
07AC7SOFTWAREASN A:120 , ASN A:122 , ASP A:157 , ASP A:159 , ASN A:163 , ASP A:215binding site for residue CA A 1003
08AC8SOFTWAREALA A:20 , HOH A:1101 , ASP D:101binding site for residue CL A 1004
09AC9SOFTWAREASN C:3 , ARG C:4 , ASP C:36 , ASP C:38 , ASP C:40 , ASP C:86binding site for residue CA C 1001
10AD1SOFTWAREGLU C:21 , ASP C:71 , GLU C:73 , ASP C:104 , HOH C:1171 , HOH C:1183binding site for residue CA C 1002
11AD2SOFTWAREGLU C:21 , GLU C:73 , ASP C:101 , VAL C:102 , ASP C:104 , ASP C:137binding site for residue CA C 1003
12AD3SOFTWAREASN C:103 , ASN C:105 , ASP C:135 , ASP C:137 , GLY C:141 , ASP C:186binding site for residue CA C 1004
13AD4SOFTWAREASN D:3 , ARG D:4 , ASP D:36 , ASP D:38 , ASP D:40 , ASP D:86binding site for residue CA D 1001
14AD5SOFTWAREGLU D:21 , ASP D:71 , GLU D:73 , ASP D:104 , HOH D:1171 , HOH D:1173binding site for residue CA D 1002
15AD6SOFTWAREGLU D:21 , GLU D:73 , ASP D:101 , VAL D:102 , ASP D:104 , ASP D:137binding site for residue CA D 1003
16AD7SOFTWAREASN D:103 , ASN D:105 , ASP D:135 , ASP D:137 , GLY D:141 , ASP D:186binding site for residue CA D 1004

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:11 -A:99
2B:11 -B:99

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Pro B:86 -Pro B:87
2Pro A:86 -Pro A:87
3Gln C:112 -Pro C:113
4Gln C:149 -Pro C:150
5Gln D:112 -Pro D:113
6Gln D:149 -Pro D:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XXW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XXW)

(-) Exons   (0, 0)

(no "Exon" information available for 4XXW)

(-) Sequences/Alignments

Asymmetric 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:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.......eee...............eeeeee.hhhh.eeee....eeee................eeeeeeeeee.....eeeeeeeeeee.......ee....eeeeee.......eee........ee...hhhhh..eeeee......hhhhhee........eee..........eeeeeeeee....hhhhh.eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xxw A   8 DDDCKLARGGPPATIVAIDEESRNGTILVDNMLIKGTAGGPDPTIELSLKDNVDYWVLLDPVKQMLFLNSTGRVLDRDPPMNIHSIVVQVQCVNKKVGTVIYHEVRIVVRDRNDNSPTFKHESYYATVNELTPVGTTIFTGFSGDNGATDIDDGPNGQIEYVIQYNPEDPTSNDTFEIPLMLTGNVVLRKRLNYEDKTRYYVIIQANDRAQNLNERRTTTTTLTVDLEH 236
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227         


Chain B from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.......eee...............eeeeee.hhhh.eeee....eeee................eeeeeeeeee.....eeeeeeeeeee.......ee....eeeeee.......eee........ee...hhhhh.eeeeee......hhhhhee........eee..........eeeeeeeeee...hhhhh.eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xxw B   8 DDDCKLARGGPPATIVAIDEESRNGTILVDNMLIKGTAGGPDPTIELSLKDNVDYWVLLDPVKQMLFLNSTGRVLDRDPPMNIHSIVVQVQCVNKKVGTVIYHEVRIVVRDRNDNSPTFKHESYYATVNELTPVGTTIFTGFSGDNGATDIDDGPNGQIEYVIQYNPEDPTSNDTFEIPLMLTGNVVLRKRLNYEDKTRYYVIIQANDRAQNLNERRTTTTTLTVDLEH 236
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227         


Chain C from PDB  Type:PROTEIN  Length:204
                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......ee.hhhhhh.eeee.......eeee..ee.......eeeeehhhhhhheee.....eeee..........eeeeeeeee....eeeeeeeeeee.......ee....eeeee........eeee..ee...hhhhhh.eeee......eee.....eeee..........eeeeeeeee........eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xxw C   1 QVNRLPFFTNHFFDTYLLISEDTPVGSSVTQLLARDMDNDPLVFGVSGEEASRFFAVEPDTGVVWLRQPLDRETKSEFTVEFSVSDHQGVITRKVNIQVGDVNDNAPTFHNQPYSVRIPENTPVGTPIFIVNATDPDLGAGGSVLYSFQPPSPFFAIDSARGIVTVIQELDYEVTQAYQLTVNATDQDKTRPLSTLANLAIIIT 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    


Chain D from PDB  Type:PROTEIN  Length:204
                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......ee.hhhhhh.eeee.......eeee..ee.......eeeeehhhhhhheee.....eeee..........eeeeeeeee....eeeeeeeeeee.......eee...eeeeee.......eeee.eee...hhhhhh.eeee......eee.....eeee..........eeeeeeeee........eeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xxw D   1 QVNRLPFFTNHFFDTYLLISEDTPVGSSVTQLLARDMDNDPLVFGVSGEEASRFFAVEPDTGVVWLRQPLDRETKSEFTVEFSVSDHQGVITRKVNIQVGDVNDNAPTFHNQPYSVRIPENTPVGTPIFIVNATDPDLGAGGSVLYSFQPPSPFFAIDSARGIVTVIQELDYEVTQAYQLTVNATDQDKTRPLSTLANLAIIIT 204
                                    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 4XXW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XXW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XXW)

(-) Gene Ontology  (47, 65)

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 Related Entries

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

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        CAD23_MOUSE | Q99PF4: 2wbx 2wcp 2wd0 2whv 3mvs 4apx 4aq8 4aqa 4aqe 4axw
        PCD15_MOUSE | Q99PJ1: 4apx 4aq8 4aqa 4aqe 4axw 5kj4

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