3BJH

Soft-SAD crystal structure of a pheromone binding protein from the honeybee Apis mellifera L.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Sulfur single-wavelength anomalous diffraction crystal structure of a pheromone-binding protein from the honeybee Apis mellifera L.

Lartigue, A.Gruez, A.Briand, L.Blon, F.Walsh, M.Pernollet, J.C.Tegoni, M.Cambillau, C.

(2004) J Biol Chem 279: 4459-4464

  • DOI: 10.1074/jbc.M311212200
  • Primary Citation of Related Structures:  
    3BJH

  • PubMed Abstract: 
  • Pheromone binding proteins (PBPs) are small helical proteins ( approximately 13-17 kDa) present in several sensory organs from moth and other insect species. They are involved in the transport of pheromones from the sensillar lymph to the olfactory receptors ...

    Pheromone binding proteins (PBPs) are small helical proteins ( approximately 13-17 kDa) present in several sensory organs from moth and other insect species. They are involved in the transport of pheromones from the sensillar lymph to the olfactory receptors. We report here the crystal structure of a PBP (Amel-ASP1) originating from the honey-bee (Apis mellifera) antennae and expressed as recombinant protein in the yeast Pichia pastoris. Crystals of Amel-ASP1 were obtained at pH 5.5 using the nano-drops technique of crystallization with a novel optimization procedure, and the structure was solved initially with the single-wavelength anomalous diffraction technique using sulfur anomalous dispersion. The structure of Amel-ASP1 has been refined at 1.6-A resolution. Its fold is roughly similar to that of other PBP/odorant binding proteins, presenting six helices and three disulfide bridges. Contrary to the PBPs from Bombyx mori (Sandler, B. H., Nikonova, L., Leal, W. S., and Clardy, J. (2000) Chem. Biol. 7, 143-151) and Leucophea maderae (Lartigue, A., Gruez, A., Spinelli, S., Riviere, S., Brossut, R., Tegoni, M., and Cambillau, C. (2003) J. Biol. Chem. 278, 30213-30218), the extended C terminus folds into the protein and forms a wall of the internal hydrophobic cavity. Its backbone groups establish two hydrogen bonds with a serendipitous ligand, n-butyl-benzene-sulfonamide, an additive used in plastics. This mode of binding might, however, mimic that used by one of the pheromonal blend components and illustrates the binding versatility of PBPs.


    Related Citations: 
    • Structural Basis of the Honey Bee PBP Pheromone and pH-induced Conformational Change
      Pesenti, M.E., Spinelli, S., Bezirard, V., Briand, L., Pernollet, J.C., Tegoni, M., Cambillau, C.
      (2008) J Mol Biol --: --

    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, Unite Mixte de Recherche 6098 CNRS and Universités Aix-Marseille I and II, 13402 Marseille Cedex 20, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pheromone-binding protein ASP1A119Apis melliferaMutation(s): 0 
Gene Names: Obp1
Find proteins for Q8WRW5 (Apis mellifera)
Explore Q8WRW5 
Go to UniProtKB:  Q8WRW5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NBB
Query on NBB

Download Ideal Coordinates CCD File 
B [auth A]N-BUTYL-BENZENESULFONAMIDE
C10 H15 N O2 S
IPRJXAGUEGOFGG-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.386α = 90
b = 86.289β = 90
c = 50.698γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance