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(-) Description

Title :  SOLUTION STRUCTURE OF MOUSE PROTOCADHERIN BETA 14 (26-137)
 
Authors :  T. Tomizawa, T. Kigawa, K. Saito, S. Koshiba, M. Inoue, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  15 Feb 05  (Deposition) - 15 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Protocadherin Beta, Ss Bond, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Nppsfa, National Project On Protein Structural And Functional Analyses, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Tomizawa, T. Kigawa, K. Saito, S. Koshiba, M. Inoue, S. Yokoyama
Solution Structure Of Mouse Protocadherin Beta 14 (26-137)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTOCADHERIN BETA 14
    Chains: A
    Engineered: YES
    Expression System Plasmid: P031215-82
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-125
    Gene: RIKEN CDNA 2210006M07
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: CELL-FREE PROTEIN SYNTHESIS

 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 1WYJ)

(-) Sites  (0, 0)

(no "Site" information available for 1WYJ)

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:78 -A:84

(-) Cis Peptide Bonds  (2, 40)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Asn A:82 -Pro A:83
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Ser A:94 -Pro A:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 3)

NMR Structure (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CADHERIN_2PS50268 Cadherins domain profile.PCDBE_MOUSE28-133
134-242
243-347
348-451
452-561
576-676		  2A:10-115
A:116-125
-
-
-
-
2CADHERIN_1PS00232 Cadherin domain signature.PCDBE_MOUSE121-131
230-240
335-345
439-449
549-559		  1A:103-113
-
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 1WYJ)

(-) 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:125
 aligned with PCDBE_MOUSE | Q6PB90 from UniProtKB/Swiss-Prot  Length:796

    Alignment length:223
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221   
          PCDBE_MOUSE     2 ETSLHKAPQKRQVTAIIFLLLLWEAGSATITYSVLEETDRGSLVGNLAKDLGLSLRELITRGAQILSKGNKQLLQLEQKSGNLLLKEKLDREELCGSTNPCILHFQVLLKSPVQFIQGEIQLQDVNDHAPEFMEDEILLKILESSLPGAVFPLKIAQDLDVGSNTVQNYTISTNAHFHLLTRNHSDGRKYPELVLDKALDREEQAQIRLTLTAMDSGSPPKTG 224
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------Cadherin_2-1wyjA01 A:11-94                                                          ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......-----------------.......eee........eeee.......hhhhhhhh..eee.......eee.....eeee....................eeee....eee...eee..............-------------------------------------------------------------------------------..--.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------CADHERIN_2  PDB: A:10-115 UniProt: 28-133                                                                 CADHERIN_2  PDB: A:116-125 UniProt: 134-242                                                 PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------CADHERIN_1 --------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wyj A   1 GSSGSSG-----------------AGSATITYSVLEETDRGSLVGNLAKDLGLSLRELITRGAQILSKGNKQLLQLEQKSGNLLLKEKLDREELCGSTNPCILHFQVLLKSPVQFIQGEIQLQDVNDHAPEFMEDE-------------------------------------------------------------------------------SG--PSSG 125
                                  |  -         -    |   13        23        33        43        53        63        73        83        93       103       113     |   -         -         -         -         -         -         -         -     ||122   
                                  7                 8                                                                                                            119                                                                             120|  |   
                                                                                                                                                                                                                                                  121  |   
                                                                                                                                                                                                                                                     122
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  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 1WYJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WYJ)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: E-set (290)

(-) Gene Ontology  (6, 6)

NMR Structure(hide GO term definitions)
Chain A   (PCDBE_MOUSE | Q6PB90)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
biological process
    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: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.
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.

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  Cis Peptide Bonds
    Asn A:82 - Pro A:83   [ RasMol ]  
    Ser A:94 - Pro A:95   [ RasMol ]  
 

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