2P70

Bombyx mori pheromone binding protein bound to bell pepper odorant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Bombyx mori pheromone-binding protein binding nonpheromone ligands: implications for pheromone recognition.

Lautenschlager, C.Leal, W.S.Clardy, J.

(2007) Structure 15: 1148-1154

  • DOI: https://doi.org/10.1016/j.str.2007.07.013
  • Primary Citation of Related Structures:  
    2P70, 2P71

  • PubMed Abstract: 

    Insect pheromone-binding proteins (PBPs) transport sex pheromones through the aqueous layer surrounding G protein-coupled receptors that initiate signaling events leading to mating. This PBP-receptor system strongly discriminates between ligands with subtle structural differences, but it has proved difficult to distinguish the degree of discrimination of the PBP from that of the G protein-coupled receptor. The three-dimensional structures of the PBP of Bombyx mori, the silkworm moth, both with and without its cognate ligand bombykol ([E,Z]-10,12-hexadecadienol), have been determined by X-ray crystallography and NMR. In this paper, the structures of the same binding protein with bound iodohexadecane and bell pepper odorant were determined at 1.9 and 2.0 A, respectively. These structures illustrate the remarkable plasticity in the ligand binding site of the PBP, but suggest the protein might still act as a filter during pheromone signal processing.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
pheromone-binding protein132Bombyx moriMutation(s): 0 
Gene Names: pheromone binding protein
UniProt
Find proteins for P34174 (Bombyx mori)
Explore P34174 
Go to UniProtKB:  P34174
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34174
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.85α = 90
b = 83.85β = 90
c = 34.82γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-10-30
    Changes: Structure summary