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(-) Description

Title :  STRUCTURE OF MOUSE BETA-NEUREXIN 2D4
 
Authors :  J. Koehnke, X. Jin, L. Shapiro
Date :  17 Dec 07  (Deposition) - 25 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Beta-Neurexin 2D4, Lns6, Lectin, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Koehnke, X. Jin, N. Trbovic, P. S. Katsamba, J. Brasch, G. Ahlsen, P. Scheiffele, B. Honig, A. G. Palmer, L. Shapiro
Crystal Structures Of Beta-Neurexin 1 And Beta-Neurexin 2 Ectodomains And Dynamics Of Splice Insertion Sequence 4.
Structure V. 16 410 2008
PubMed-ID: 18334216  |  Reference-DOI: 10.1016/J.STR.2007.12.024

(-) Compounds

Molecule 1 - BETA-NEUREXIN 2D4
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PGEX-NRX2D4
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: LNS DOMAIN
    Gene: NRXN2
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3BOP)

(-) Sites  (0, 0)

(no "Site" information available for 3BOP)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BOP)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:223 -Arg A:224
2Ser B:135 -Gly B:136
3Gly C:94 -Gly C:95
4Gly C:136 -Leu C:137

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BOP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BOP)

(-) Exons   (0, 0)

(no "Exon" information available for 3BOP)

(-) 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:168
 aligned with Q3TQ54_MOUSE | Q3TQ54 from UniProtKB/TrEMBL  Length:353

    Alignment length:175
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255     
         Q3TQ54_MOUSE    86 GTTYIFGKGGALITYTWPPNDRPSTRMDRLAVGFSTHQRSAVLVRVDSASGLGDYLQLHIDQGTVGVIFNVGTDDITIDEPNAIVSDGKYHVVRFTRSGGNATLQVDSWPVNERYPAGRQLTIFNSQAAIKIGGRDQGRPFQGQVSGLYYNGLKVLALAAESDPNVRTEGHLRLV 260
               SCOP domains d3bopa_ A: automated matches                                                                                                                                                    SCOP domains
               CATH domains 3bopA00 A:86-260  [code=2.60.120.200, no name defined]                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....eeeee............eeeeeee.....eeeeeeee.....eeeeeeee..eeeeeeee..eeeeeee..........eeeeeeee..eeeeee..eeeee....-------..eeeeeee.........eeeeeeee...hhhhhhhh....eeee..eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bop A  86 ATTYIFGKGGALITYTWPPNDRPSTRMDRLAVGFSTHQRSAVLVRVDSASGLGDYLQLHIDQGTVGVIFNVGTDDITIDEPNAIVSDGKYHVVRFTRSGGNATLQVDSWPVNERYPA-------NSQAAIKIGGRDQGRPFQGQVSGLYYNGLKVLALAAESDPNVRTEGHLRLV 260
                                    95       105       115       125       135       145       155       165       175       185       195      |  -    |  215       225       235       245       255     
                                                                                                                                              202     210                                                  


Chain B from PDB  Type:PROTEIN  Length:168
 aligned with Q3TQ54_MOUSE | Q3TQ54 from UniProtKB/TrEMBL  Length:353

    Alignment length:174
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256    
         Q3TQ54_MOUSE    87 TTYIFGKGGALITYTWPPNDRPSTRMDRLAVGFSTHQRSAVLVRVDSASGLGDYLQLHIDQGTVGVIFNVGTDDITIDEPNAIVSDGKYHVVRFTRSGGNATLQVDSWPVNERYPAGRQLTIFNSQAAIKIGGRDQGRPFQGQVSGLYYNGLKVLALAAESDPNVRTEGHLRLV 260
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3bopB00 B:87-260  [code=2.60.120.200, no name defined]                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee............eeeeeee.....eeeeeeee.....eeeeeeee..eeeeeeee..eeeeeeeeeee......eeeeeeee..eeeeee..eeeee...------....eeeeeee.........eeeeeeee...hhhhhhhh....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bop B  87 TTYIFGKGGALITYTWPPNDRPSTRMDRLAVGFSTHQRSAVLVRVDSASGLGDYLQLHIDQGTVGVIFNVGTDDITIDEPNAIVSDGKYHVVRFTRSGGNATLQVDSWPVNERYP------IFNSQAAIKIGGRDQGRPFQGQVSGLYYNGLKVLALAAESDPNVRTEGHLRLV 260
                                    96       106       116       126       136       146       156       166       176       186       196    |    - |     216       226       236       246       256    
                                                                                                                                            201    208                                                    


Chain C from PDB  Type:PROTEIN  Length:169
 aligned with Q3TQ54_MOUSE | Q3TQ54 from UniProtKB/TrEMBL  Length:353

    Alignment length:175
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255     
         Q3TQ54_MOUSE    86 GTTYIFGKGGALITYTWPPNDRPSTRMDRLAVGFSTHQRSAVLVRVDSASGLGDYLQLHIDQGTVGVIFNVGTDDITIDEPNAIVSDGKYHVVRFTRSGGNATLQVDSWPVNERYPAGRQLTIFNSQAAIKIGGRDQGRPFQGQVSGLYYNGLKVLALAAESDPNVRTEGHLRLV 260
               SCOP domains d3bopc_ C: automated matches                                                                                                                                                    SCOP domains
               CATH domains 3bopC00 C:86-260  [code=2.60.120.200, no name defined]                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....eeeee...........eeeeeeeee....eeeeeeee.......eeeeee..eeeeeeee..eeeeeee.........eeeeeeee....eeeee..eeeee.....------..eeeeeee.ee..ee..eee...ee...hhhhhhhh....eeee..eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bop C  86 ATTYIFGKGGALITYTWPPNDRPSTRMDRLAVGFSTHQRSAVLVRVDSASGLGDYLQLHIDQGTVGVIFNVGTDDITIDEPNAIVSDGKYHVVRFTRSGGNATLQVDSWPVNERYPAG------NSQAAIKIGGRDQGRPFQGQVSGLYYNGLKVLALAAESDPNVRTEGHLRLV 260
                                    95       105       115       125       135       145       155       165       175       185       195       | -    |  215       225       235       245       255     
                                                                                                                                               203    210
   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  (1, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BOP)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q3TQ54_MOUSE | Q3TQ54)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
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.

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  Cis Peptide Bonds
    Gly A:223 - Arg A:224   [ RasMol ]  
    Gly C:136 - Leu C:137   [ RasMol ]  
    Gly C:94 - Gly C:95   [ RasMol ]  
    Ser B:135 - Gly B:136   [ RasMol ]  
 
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3bod STRUCTURE OF NEUREXIN 1D4