3CYZ

Dimeric crystal structure of a pheromone binding protein from Apis mellifera in complex with 9-keto-2(E)-decenoic acid at pH 7.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Queen bee pheromone binding protein pH-induced domain swapping favors pheromone release

Pesenti, M.E.Spinelli, S.Bezirard, V.Briand, L.Pernollet, J.C.Campanacci, V.Tegoni, M.Cambillau, C.

(2009) J.Mol.Biol. 390: 981-990

  • DOI: 10.1016/j.jmb.2009.05.067
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In honeybee (Apis mellifera) societies, the queen controls the development and the caste status of the members of the hive. Queen bees secrete pheromonal blends comprising 10 or more major and minor components, mainly hydrophobic. The major component ...

    In honeybee (Apis mellifera) societies, the queen controls the development and the caste status of the members of the hive. Queen bees secrete pheromonal blends comprising 10 or more major and minor components, mainly hydrophobic. The major component, 9-keto-2(E)-decenoic acid (9-ODA), acts on the workers and male bees (drones), eliciting social or sexual responses. 9-ODA is captured in the antennal lymph and transported to the pheromone receptor(s) in the sensory neuron membranes by pheromone binding proteins (PBPs). A key issue is to understand how the pheromone, once tightly bound to its PBP, is released to activate the receptor. We report here on the structure at physiological pH of the main antennal PBP, ASP1, identified in workers and male honeybees, in its apo or complexed form, particularly with the main component of the queen mandibular pheromonal mixture (9-ODA). Contrary to the ASP1 structure at low pH, the ASP1 structure at pH 7.0 is a domain-swapped dimer with one or two ligands per monomer. This dimerization is disrupted by a unique residue mutation since Asp35 Asn and Asp35 Ala mutants remain monomeric at pH 7.0, as does native ASP1 at pH 4.0. Asp35 is conserved in only approximately 30% of medium-chain PBPs and is replaced by other residues, such as Asn, Ala and Ser, among others, thus excluding that they may perform domain swapping. Therefore, these different medium-chain PBPs, as well as PBPs from moths, very likely exhibit different mechanisms of ligand release or receptor recognition.


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, UMR CNRS, Marseille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pheromone-binding protein ASP1
A, B
119Apis melliferaMutation(s): 0 
Find proteins for Q9U9J6 (Apis mellifera)
Go to UniProtKB:  Q9U9J6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
9OD
Query on 9OD

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A, B
(2Z)-9-oxodec-2-enoic acid
9-keto-2(E)-decenoic acid
C10 H16 O3
INJRDZMWIAYEMM-VURMDHGXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9ODKd: 60 nM BINDINGMOAD
9ODKd: 60 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.285α = 90.00
b = 75.555β = 90.00
c = 84.113γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance