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(-) Description

Title :  CRYSTAL STRUCTURE OF NECTIN-LIKE MOLECULE-1 PROTEIN DOMAIN 1
 
Authors :  X. Dong, F. Xu, Y. Gong, J. Gao, P. Lin, T. Chen, Y. Peng, B. Qiang, J. Yuan, X. Peng, Z. Rao
Date :  03 Apr 05  (Deposition) - 07 Feb 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nectin-Like, Ig-Like Domain, V Domain, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Dong, F. Xu, Y. Gong, J. Gao, P. Lin, T. Chen, Y. Peng, B. Qiang, J. Yuan, X. Peng, Z. Rao
Crystal Structure Of The V Domain Of Human Nectin-Like Molecule-1/Syncam3/Tsll1/Igsf4B, A Neural Tissue-Specific Immunoglobulin-Like Cell-Cell Adhesion Molecule
J. Biol. Chem. V. 281 10610 2006
PubMed-ID: 16467305  |  Reference-DOI: 10.1074/JBC.M513459200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GAPA225
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET32A
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRESIDUES 37-141
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNECTIN-LIKE MOLECULE_1 DOMAIN 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1Z9M)

(-) Sites  (0, 0)

(no "Site" information available for 1Z9M)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:60 -A:120
2B:60 -B:120

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Met A:125 -Pro A:126
2Met B:125 -Pro B:126

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z9M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z9M)

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003681251aENSE00001446374chr1:159141399-159141643245CADM3_HUMAN1-30302A:38-40
B:37-40
3
4
1.3ENST000003681253ENSE00001067902chr1:159161726-159161866141CADM3_HUMAN30-77482A:40-87
B:40-87
48
48
1.4ENST000003681254ENSE00001067906chr1:159162368-159162520153CADM3_HUMAN77-128522A:87-138
B:87-138
52
52
1.5ENST000003681255ENSE00001067908chr1:159163213-159163350138CADM3_HUMAN128-174472A:138-141
B:138-141
4
4
1.6bENST000003681256bENSE00001067905chr1:159163660-159163830171CADM3_HUMAN174-231580--
1.7ENST000003681257ENSE00001067909chr1:159166154-15916624491CADM3_HUMAN231-261310--
1.8cENST000003681258cENSE00001067900chr1:159166681-159166850170CADM3_HUMAN261-318580--
1.9ENST000003681259ENSE00001067907chr1:159169541-159169666126CADM3_HUMAN318-360430--
1.10cENST0000036812510cENSE00001446369chr1:159170594-1591731032510CADM3_HUMAN360-398390--

(-) 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:104
 aligned with CADM3_HUMAN | Q8N126 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:104
                                    37        47        57        67        77        87        97       107       117       127    
          CADM3_HUMAN    28 QDDSQPWTSDETVVAGGTVVLKCQVKDHEDSSLQWSNPAQQTLYFGEKRALRDNRIQLVTSTPHELSISISNVALADEGEYTCSIFTMPVRTAKSLVTVLGIPQ 131
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee....eeeeee........eeee.....eeee..ee......eeeeee...eeeeee...hhhhheeeeeee.....eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1----------------------------------------------Exon 1.4  PDB: A:87-138 UniProt: 77-128             --- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.3  PDB: A:40-87 UniProt: 30-77           --------------------------------------------------1.5  Transcript 1 (2)
                 1z9m A  38 QDDSQPWTSDETVVAGGTVVLKCQVKDHEDSSLQWSNPAQQTLYFGEKRALRDNRIQLVTSTPHELSISISNVALADEGEYTCSIFTMPVRTAKSLVTVLGIPQ 141
                                    47        57        67        77        87        97       107       117       127       137    

Chain B from PDB  Type:PROTEIN  Length:105
 aligned with CADM3_HUMAN | Q8N126 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:105
                                    36        46        56        66        76        86        96       106       116       126     
          CADM3_HUMAN    27 SQDDSQPWTSDETVVAGGTVVLKCQVKDHEDSSLQWSNPAQQTLYFGEKRALRDNRIQLVTSTPHELSISISNVALADEGEYTCSIFTMPVRTAKSLVTVLGIPQ 131
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) V-set-1z9mB01 B:37-137                                                                               ---- Pfam domains (1)
           Pfam domains (2) V-set-1z9mB02 B:37-137                                                                               ---- Pfam domains (2)
         Sec.struct. author ...........eeee....eeeeee........eeee.....eeee..ee......eeeeeee..eeeeee...hhhhheeeeeee.....eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1a----------------------------------------------Exon 1.4  PDB: B:87-138 UniProt: 77-128             --- Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.3  PDB: B:40-87 UniProt: 30-77           --------------------------------------------------1.5  Transcript 1 (2)
                 1z9m B  37 SQDDSQPWTSDETVVAGGTVVLKCQVKDHEDSSLQWSNPAQQTLYFGEKRALRDNRIQLVTSTPHELSISISNVALADEGEYTCSIFTMPVRTAKSLVTVLGIPQ 141
                                    46        56        66        76        86        96       106       116       126       136     

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 1Z9M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Z9M)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Ig (577)
(-)
Family: V-set (144)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CADM3_HUMAN | Q8N126)
molecular function
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0034332    adherens junction organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an adherens junction. An adherens junction is a cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments.
    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:0008037    cell recognition    The process in which a cell in an organism interprets its surroundings.
    GO:0007157    heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules    The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
    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:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
cellular component
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0005913    cell-cell adherens junction    An adherens junction which connects a cell to another cell.
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    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:0005887    integral component of plasma membrane    The component of the plasma 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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    Met A:125 - Pro A:126   [ RasMol ]  
    Met B:125 - Pro B:126   [ RasMol ]  
 

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