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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE PROTOCADHERIN-15 EC9-10
 
Authors :  R. Araya-Secchi, M. Sotomayor
Date :  17 Jun 16  (Deposition) - 23 Nov 16  (Release) - 23 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Hearing, Mechanotransduction, Adhesion, Calcium-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Araya-Secchi, M. Sotomayor
Structure Of Inner-Ear Protocadherin-15 Fragment (Ec8-10) Reveals An Atypical Calcium Free Linker
Nat Commun 2016
PubMed: search  |  Reference-DOI: 10.1038/NCOMMS13458

(-) Compounds

Molecule 1 - PROTOCADHERIN-15
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Strain: BL21
    Expression System Taxid: 866768
    Fragment: CADHERIN 9 AND 10, RESIDUES 924-1149
    Gene: PCDH15
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1CA12Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:899 , TYR A:901 , ASP A:931 , ASP A:933 , ALA A:939 , ASP A:989binding site for residue CA A 2001
02AC2SOFTWAREGLU A:1026 , GLU A:1077 , ASP A:1115 , GLU A:1116 , ASP A:1118binding site for residue CA A 2002
03AC3SOFTWAREGLU A:1026 , ASP A:1075 , ASP A:1118binding site for residue CA A 2003
04AC4SOFTWAREASN B:899 , TYR B:901 , ASP B:931 , ASP B:933 , ALA B:939 , ASP B:989binding site for residue CA B 2001
05AC5SOFTWAREGLU B:1026 , GLU B:1077 , ASP B:1115 , GLU B:1116 , ASP B:1118 , CA B:2003binding site for residue CA B 2002
06AC6SOFTWAREGLU B:1026 , ASP B:1075 , GLU B:1077 , ASP B:1118 , CA B:2002binding site for residue CA B 2003
07AC7SOFTWAREASN C:899 , TYR C:901 , ASP C:931 , ASP C:933 , ALA C:939 , ASP C:989binding site for residue CA C 2001
08AC8SOFTWAREGLU C:1026 , GLU C:1077 , ASP C:1115 , GLU C:1116 , ASP C:1118binding site for residue CA C 2002
09AC9SOFTWAREGLU C:1026 , ASP C:1075 , GLU C:1077 , ASP C:1118binding site for residue CA C 2003
10AD1SOFTWAREASN D:899 , TYR D:901 , ASP D:931 , ASP D:933 , ALA D:939 , ASP D:989binding site for residue CA D 2001
11AD2SOFTWAREGLU D:1026 , GLU D:1077 , ASP D:1115 , GLU D:1116 , ASP D:1118binding site for residue CA D 2002
12AD3SOFTWAREGLU D:1026 , ASP D:1075 , GLU D:1077 , ASP D:1118binding site for residue CA D 2003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KJ4)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:992 -Pro A:993
2Glu B:992 -Pro B:993
3Glu C:992 -Pro C:993
4Glu D:992 -Pro D:993

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KJ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KJ4)

(-) Exons   (0, 0)

(no "Exon" information available for 5KJ4)

(-) 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:228
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee...eeeeee........eeee..eee.....hhhhh.eeeee...hhhhhhheee.....eeee..........eeeeeeeee.......eeeeeeeeee.......ee...ee....ee.......eeee..ee.....eeeeeee......eee.....eeee..........eeeeeeeeeehhhhhh.....hhh.eeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5kj4 A  898 MNDYPPVFSKRIYKGMVAPDAVKGTPITTVYAEDADPPGMPASRVRYRVDDVQFPYPASIFDVEEDSGRVVTRVNLNEEPTTIFKLVVVAFDDGEPVMSSSATVRILVLHPGEIPRFTQEEYRPPPVSELAARGTVVGVISAAAINQSIVYSIVAGNEEDKFGINNVTGVIYVNSPLDYETRTSYVLRVQADSLEVVLANLRVPSKSNTAKVYIEIQDENDHPPVFLE 1125
                                   907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117        


Chain B from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee...eeeeee........eeee..eee.....hhhhh.eeeee...hhhhhhheee.....eeee..........eeeeeeeee.......eeeeeeeeee.......ee...ee....ee.......eeee..ee.....eeeeeee......eee.....eeee..........eeeeeeeeeehhhhhh.....hhh.eeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5kj4 B  898 MNDYPPVFSKRIYKGMVAPDAVKGTPITTVYAEDADPPGMPASRVRYRVDDVQFPYPASIFDVEEDSGRVVTRVNLNEEPTTIFKLVVVAFDDGEPVMSSSATVRILVLHPGEIPRFTQEEYRPPPVSELAARGTVVGVISAAAINQSIVYSIVAGNEEDKFGINNVTGVIYVNSPLDYETRTSYVLRVQADSLEVVLANLRVPSKSNTAKVYIEIQDENDHPPVFLE 1125
                                   907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117        


Chain C from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee...eeeeee........eeee..eee.....hhhhh.eeeee...hhhhhhheee.....eeee..........eeeeeeeee.......eeeeeeeeee.......ee...ee....ee.......eeee..ee.....eeeeeee......eee.....eeee..........eeeeeeeeeehhhhhh.....hhh.eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5kj4 C  898 MNDYPPVFSKRIYKGMVAPDAVKGTPITTVYAEDADPPGMPASRVRYRVDDVQFPYPASIFDVEEDSGRVVTRVNLNEEPTTIFKLVVVAFDDGEPVMSSSATVRILVLHPGEIPRFTQEEYRPPPVSELAARGTVVGVISAAAINQSIVYSIVAGNEEDKFGINNVTGVIYVNSPLDYETRTSYVLRVQADSLEVVLANLRVPSKSNTAKVYIEIQDENDH 1119
                                   907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117  


Chain D from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee...eeeeee........eeee..eee.....hhhhh.eeeee...hhhhhhheee.....eeee..........eeeeeeeee.......eeeeeeeeee.......ee...ee....ee.......eeee..ee.....eeeeeee......eee.....eeee..........eeeeeeeeeehhhhhh.....hhh.eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5kj4 D  898 MNDYPPVFSKRIYKGMVAPDAVKGTPITTVYAEDADPPGMPASRVRYRVDDVQFPYPASIFDVEEDSGRVVTRVNLNEEPTTIFKLVVVAFDDGEPVMSSSATVRILVLHPGEIPRFTQEEYRPPPVSELAARGTVVGVISAAAINQSIVYSIVAGNEEDKFGINNVTGVIYVNSPLDYETRTSYVLRVQADSLEVVLANLRVPSKSNTAKVYIEIQDENDH 1119
                                   907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117
   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 5KJ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KJ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KJ4)

(-) Gene Ontology  (37, 37)

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        PCD15_MOUSE | Q99PJ1: 4apx 4aq8 4aqa 4aqe 4axw 4xxw

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