1E5P

Crystal structure of aphrodisin, a sex pheromone from female hamster


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of aphrodisin, a sex pheromone from female hamster.

Vincent, F.Lobel, D.Brown, K.Spinelli, S.Grote, P.Breer, H.Cambillau, C.Tegoni, M.

(2001) J Mol Biol 305: 459-469

  • DOI: 10.1006/jmbi.2000.4241
  • Primary Citation of Related Structures:  
    1E5P

  • PubMed Abstract: 
  • We have solved the crystal structure of aphrodisin, a pheromonal protein inducing a copulatory behaviour in male hamster, using MAD methods with selenium, at 1.63 A resolution. The monomeric protein belongs to the lipocalin family, and possesses a disulfide bridge in a loop between strands 2 and 3 ...

    We have solved the crystal structure of aphrodisin, a pheromonal protein inducing a copulatory behaviour in male hamster, using MAD methods with selenium, at 1.63 A resolution. The monomeric protein belongs to the lipocalin family, and possesses a disulfide bridge in a loop between strands 2 and 3. This disulfide bridge is characteristic of a family of lipocalins mainly identified in rodents, and is analogous to the fifth disulfide bridge of the long neurotoxins, such as alpha cobratoxin. An elongated electron density was found inside the buried cavity, which might represent a serendipitous ligand of unknown origin. The analysis of the water accessible surfaces of the side-chains bordering the cavity indicates that Phe76 may be the door for the natural ligand to access the cavity. This residue defines the entry of the cavity as belonging to the consensus for lipocalins. The face bearing Phe76 might also serve for the interaction with the receptor.


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS et Universités d'Aix-Marseille I & II, 31 Chemin Joseph Aiguier, 13402, Marseille, CEDEX 20, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
APHRODISINA, B, C, D151Mesocricetus auratusMutation(s): 3 
Gene Names: MESOCRICETUS AURATUS APHRODISIN GENE
UniProt
Find proteins for P09465 (Cricetus cricetus)
Explore P09465 
Go to UniProtKB:  P09465
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.05α = 90
b = 48.92β = 102.63
c = 123.547γ = 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: 2001-07-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-09-18
    Changes: Advisory, Data collection, Database references, Derived calculations, Experimental preparation