6QQ4

Odorant-binding protein dmelOBP28a from Drosophila melanogaster


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Drosophila odorant-binding protein 28a is involved in the detection of the floral odour ss-ionone.

Gonzalez, D.Rihani, K.Neiers, F.Poirier, N.Fraichard, S.Gotthard, G.Chertemps, T.Maibeche, M.Ferveur, J.F.Briand, L.

(2020) Cell Mol Life Sci 77: 2565-2577

  • DOI: https://doi.org/10.1007/s00018-019-03300-4
  • Primary Citation of Related Structures:  
    6QQ4

  • PubMed Abstract: 

    Odorant-binding proteins (OBPs) are small soluble proteins that are thought to transport hydrophobic odorants across the aqueous sensillar lymph to olfactory receptors. A recent study revealed that OBP28a, one of the most abundant Drosophila OBPs, is not required for odorant transport, but acts in buffering rapid odour variation in the odorant environment. To further unravel and decipher its functional role, we expressed recombinant OBP28a and characterized its binding specificity. Using a fluorescent binding assay, we found that OBP28a binds a restricted number of floral-like chemicals, including ß-ionone, with an affinity in the micromolar range. We solved the X-ray crystal structure of OBP28a, which showed extensive conformation changes upon ligand binding. Mutant flies genetically deleted for the OBP28a gene showed altered responses to ß-ionone at a given concentration range, supporting its essential role in the detection of specific compounds present in the natural environment of the fly.


  • Organizational Affiliation

    AgroSup Dijon, CNRS, INRA, Université de Bourgogne-Franche Comté, Centre des Sciences du Goût et de l'Alimentation, 21000, Dijon, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
General odorant-binding protein 28a
A, B
121Drosophila melanogasterMutation(s): 0 
Gene Names: Obp28aPbprp5CG6641
UniProt
Find proteins for P54195 (Drosophila melanogaster)
Explore P54195 
Go to UniProtKB:  P54195
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54195
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
C [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
MLA
Query on MLA

Download Ideal Coordinates CCD File 
D [auth B]MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.5α = 90
b = 83.2β = 99
c = 45.6γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
PHASERphasing
MrBUMPphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FranceBURGUNDY COUNCIL

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Advisory, Data collection, Database references, Refinement description