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(-) Description

Title :  CRYSTAL STRUCTURE OF A PHEROMONE BINDING PROTEIN FROM APIS MELLIFERA IN COMPLEX WITH THE QUEEN MANDIBULAR PHEROMONE
 
Authors :  M. E. Pesenti, S. Spinelli, V. Bezirard, L. Briand, J. C. Pernollet, M. T C. Cambillau
Date :  21 Nov 07  (Deposition) - 10 Jun 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Honeybee, Apis Mellifera, Pheromone Binding Protein, Signal Transduction, Queen Mandibular Pheromone, Pheromone-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Pesenti, S. Spinelli, V. Bezirard, L. Briand, J. C. Pernollet, M. Tegoni, C. Cambillau
Structural Basis Of The Honey Bee Pbp Pheromone And Ph-Induced Conformational Change
J. Mol. Biol. V. 380 158 2008
PubMed-ID: 18508083  |  Reference-DOI: 10.1016/J.JMB.2008.04.048

(-) Compounds

Molecule 1 - PHEROMONE-BINDING PROTEIN ASP1
    Chains: A
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PHIL-D2
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 26-144
    Organism Common: HONEYBEE
    Organism Scientific: APIS MELLIFERA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
19OD1Ligand/Ion(2Z)-9-OXODEC-2-ENOIC ACID
2GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:12 , LEU A:52 , PHE A:56 , LEU A:73 , ILE A:119 , HOH A:154BINDING SITE FOR RESIDUE 9OD A 120
2AC2SOFTWAREMET A:70 , PHE A:117BINDING SITE FOR RESIDUE GOL A 121

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:20 -A:51
2A:47 -A:98
3A:89 -A:107

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:90 -Pro A:91

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BFA)

(-) 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:117
 aligned with Q8WRW5_APIME | Q8WRW5 from UniProtKB/TrEMBL  Length:144

    Alignment length:117
                                    37        47        57        67        77        87        97       107       117       127       137       
         Q8WRW5_APIME    28 DWVPPEVFDLVAEDKARCMSEHGTTQAQIDDVDKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 144
               SCOP domains d3bfaa_ A: Pheromone-binding protein asp1                                                                             SCOP domains
               CATH domains 3bfaA00 A:3-119  [code=1.10.238.20, no name defined]                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhh.........hhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3bfa A   3 DWVPPEVFDLVAEDKARCMSEHGTTQAQIDDVDKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 119
                                    12        22        32        42        52        62        72        82        92       102       112       


Chain A from PDB  Type:PROTEIN  Length:117
 aligned with Q9U9J6_APIME | Q9U9J6 from UniProtKB/TrEMBL  Length:144

    Alignment length:117
                                    37        47        57        67        77        87        97       107       117       127       137       
         Q9U9J6_APIME    28 DWVPPEVFDLVAEDKARCMSEHGTTQAQIDDVDKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 144
               SCOP domains d3bfaa_ A: Pheromone-binding protein asp1                                                                             SCOP domains
               CATH domains 3bfaA00 A:3-119  [code=1.10.238.20, no name defined]                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhh.........hhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3bfa A   3 DWVPPEVFDLVAEDKARCMSEHGTTQAQIDDVDKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 119
                                    12        22        32        42        52        62        72        82        92       102       112
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9U9J6_APIME | Q9U9J6)
molecular function
    GO:0005549    odorant binding    Interacting selectively and non-covalently with an odorant, any substance capable of stimulating the sense of smell.

Chain A   (Q8WRW5_APIME | Q8WRW5)
molecular function
    GO:0005549    odorant binding    Interacting selectively and non-covalently with an odorant, any substance capable of stimulating the sense of smell.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9U9J6_APIME | Q9U9J6: 2h8v 3bjh 3cab 3cdn
UniProtKB/TrEMBL
        Q8WRW5_APIME | Q8WRW5: 2h8v 3bjh 3cab 3cdn
        Q9U9J6_APIME | Q9U9J6: 3bfb 3bfh 3cyz 3cz0 3cz1 3cz2 3d73 3d74 3d75 3d76 3d77 3d78 3fe6 3fe8 3fe9

(-) Related Entries Specified in the PDB File

1r5r THE SAME PROTEIN COMPLEXED WITH N-BUTYL BENZENESULFONAMIDE
2h8v UNCOMPLEXED FORM OF THE SAME PROTEIN
3bfb THE SAME PROTEIN IN COMPLEX WITH THE 9-KETO-2(E)-DECENOIC ACID
3bfh THE SAME PROTEIN COMPLEXED WITH HEXADECANOIC ACID