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(-) Description

Title :  CRYSTAL STRUCTURE OF A PHEROMONE BINDING PROTEIN FROM APIS MELLIFERA WITH A SERENDIPITOUS LIGAND AT PH 5.5
 
Authors :  M. E. Pesenti, S. Spinelli, V. Bezirard, L. Briand, J. C. Pernollet, M. T C. Cambillau
Date :  27 Nov 08  (Deposition) - 01 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Pheromone Binding Protein, Honey Bee, Apis Mellifera, Signal Transduction, Queen Mandibular Pheromone, Ph (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Pesenti, S. Spinelli, V. Bezirard, L. Briand, J. C. Pernollet, M. Tegoni, C. Cambillau
Queen Bee Pheromone Binding Protein Ph Induced Domain-Swapping Favors Pheromone Release
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHEROMONE-BINDING PROTEIN ASP1
    Chains: A
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PHIL-D2
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 26-144
    Organism Common: HONEYBEE
    Organism Scientific: APIS MELLIFERA
    Organism Taxid: 7460

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CMJ1Ligand/Ion(20S)-20-METHYLDOTETRACONTANE
3GOL1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:53 , PHE A:56 , MET A:70 , LEU A:73 , VAL A:85 , MET A:86 , VAL A:115 , TRP A:116 , PHE A:117BINDING SITE FOR RESIDUE CMJ A 120
2AC2SOFTWAREASN A:41 , TYR A:102 , HOH A:157 , HOH A:328BINDING SITE FOR RESIDUE GOL A 121
3AC3SOFTWAREASN A:64 , VAL A:65 , LEU A:90 , THR A:92 , HOH A:211BINDING SITE FOR RESIDUE CL A 122

(-) 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 3FE6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FE6)

(-) Exons   (0, 0)

(no "Exon" information available for 3FE6)

(-) 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 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 d3fe6a_ A: Pheromone-binding protein asp1                                                                             SCOP domains
               CATH domains 3fe6A00 A:3-119  [code=1.10.238.20, no name defined]                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3fe6 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 3FE6)

(-) Gene Ontology  (1, 1)

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.

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    Leu A:90 - Pro A:91   [ RasMol ]  
 

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  3fe6
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2h8v THE SAME PROTEIN IN APO FORM AT PH 5.5
3bfa THE SAME PROTEIN IN COMPLEX WITH THE QMP AT PH 5.5
3bfb THE SAME PROTEIN IN COMPLEX WITH THE 9-ODA AT PH 5.5
3bfh THE SAME PROTEIN IN COMPLEX WITH THE HDOA AT PH 5.5
3bjh THE SAME PROTEIN IN COMPLEX WITH THE NBBSA AT PH 5.5
3cab THE SAME PROTEIN IN COMPLEX WITH THE NBBSA SOAKED AT PH 7.0
3cdn THE SAME PROTEIN IN APO FORM SOAKED AT PH 4.0
3cyz THE SAME PROTEIN IN COMPLEX WITH THE 9-ODA AT PH 7.0
3cz0 THE SAME PROTEIN IN COMPLEX WITH THE QMP AT PH 7.0
3cz1 THE SAME PROTEIN IN COMPLEX WITH THE NBBSA AT PH 7.0
3cz2 THE SAME PROTEIN IN APO FORM AT PH 7.0
3d73 THE MUTANT D35A OF THE SAME PROTEIN AT PH 7.0
3d74 THE MUTANT D35A OF THE SAME PROTEIN SOAKED AT PH 5.5
3d75 THE MUTANT D35N OF THE SAME PROTEIN AT PH 5.5
3d76 THE MUTANT D35N OF THE SAME PROTEIN SOAKED AT PH 7.0
3d77 THE MUTANT D35N OF THE SAME PROTEIN SOAKED AT PH 4.0
3d78 THE MUTANT D35N OF THE SAME PROTEIN AT PH 7.0
3fe8 THE SAME PROTEIN IN COMPLEX WITH A SERENDIPITOUS LIGAND SOAKED AT PH 4.0
3fe9 THE SAME PROTEIN IN COMPLEX WITH A SERENDIPITOUS LIGAND SOAKED AT PH 7.0