3S0D

Apis mellifera OBP 14 in complex with the citrus odorant citralva (3,7-dimethylocta-2,6-dienenitrile)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of Apis mellifera OBP14, a C-minus odorant-binding protein, and its complexes with odorant molecules.

Spinelli, S.Lagarde, A.Iovinella, I.Legrand, P.Tegoni, M.Pelosi, P.Cambillau, C.

(2012) Insect Biochem Mol Biol 42: 41-50

  • DOI: https://doi.org/10.1016/j.ibmb.2011.10.005
  • Primary Citation of Related Structures:  
    3RZS, 3S0A, 3S0B, 3S0D, 3S0E, 3S0F, 3S0G

  • PubMed Abstract: 

    Apis mellifera (Amel) relies on its olfactory system to detect and identify new-sources of floral food. The Odorant-Binding Proteins (OBPs) are the first proteins involved in odorant recognition and interaction, before activation of the olfactory receptors. The Amel genome possess a set of 21 OBPs, much fewer compared to the 60-70 OBPs found in Diptera genomes. We have undertaken a structural proteomics study of Amel OBPs, alone or in complex with odorant or model compounds. We report here the first 3D structure of a member of the C-minus class OBPs, AmelOBP14, characterized by only two disulfide bridges of the three typical of classical OBPs. We show that AmelOBP14 possesses a core of 6 α-helices comparable to that of classical OBPs, and an extra exposed C-terminal helix. Its binding site is located within this core and is completely closed. Fluorescent experiments using 1-NPN displacement demonstrate that AmelOBP14 is able to bind several compounds with sub micromolar dissociation constants, among which citralva and eugenol exhibit the highest affinities. We have determined the structures of AmelOBP14 in complex with 1-NPN, eugenol and citralva, explaining their strong binding. Finally, by introducing a double cysteine mutant at positions 44 and 97, we show that a third disulfide bridge was formed in the same position as in classical OBPs without disturbing the fold of AmelOBP14.


  • Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS and Universités of Marseille, 163 Av. de Luminy Case 932, 13288 Marseille Cedex 09, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OBP14119Apis melliferaMutation(s): 0 
Gene Names: NP_001035313
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CTV
Query on CTV

Download Ideal Coordinates CCD File 
B [auth A](2Z)-3,7-dimethylocta-2,6-dienenitrile
C10 H15 N
HLCSDJLATUNSSI-YFHOEESVSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CTV PDBBind:  3S0D Kd: 90 (nM) from 1 assay(s)
Binding MOAD:  3S0D Kd: 280 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.4α = 90
b = 37.86β = 90
c = 86.15γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-30
    Type: Initial release
  • Version 1.1: 2012-01-11
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description