7NZA

Structure of OBP1 from Varroa destructor, form P2<1>


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A new non-classical fold of varroa odorant-binding proteins reveals a wide open internal cavity.

Amigues, B.Zhu, J.Gaubert, A.Arena, S.Renzone, G.Leone, P.Fischer, I.M.Paulsen, H.Knoll, W.Scaloni, A.Roussel, A.Cambillau, C.Pelosi, P.

(2021) Sci Rep 11: 13172-13172

  • DOI: https://doi.org/10.1038/s41598-021-92604-2
  • Primary Citation of Related Structures:  
    7NYJ, 7NZA

  • PubMed Abstract: 

    Odorant-binding proteins (OBPs), as they occur in insects, form a distinct class of proteins that apparently has no closely related representatives in other animals. However, ticks, mites, spiders and millipedes contain genes encoding proteins with sequence similarity to insect OBPs. In this work, we have explored the structure and function of such non-insect OBPs in the mite Varroa destructor, a major pest of honey bee. Varroa OBPs present six cysteines paired into three disulphide bridges, but with positions in the sequence and connections different from those of their insect counterparts. VdesOBP1 structure was determined in two closely related crystal forms and appears to be a monomer. Its structure assembles five α-helices linked by three disulphide bridges, one of them exhibiting a different connection as compared to their insect counterparts. Comparison with classical OBPs reveals that the second of the six α-helices is lacking in VdesOBP1. Ligand-binding experiments revealed molecules able to bind only specific OBPs with a moderate affinity, suggesting that either optimal ligands have still to be identified, or post-translational modifications present in the native proteins may be essential for modulating binding activity, or else these OBPs might represent a failed attempt in evolution and are not used by the mites.


  • Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques (AFMB, UMR 6098), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université (AMU), Campus 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
Odorant Binding Protein from Varroa destructor, form P2<1>
A, B
147Varroa destructorMutation(s): 0 
UniProt
Find proteins for A0A7M7KVA6 (Varroa destructor)
Explore A0A7M7KVA6 
Go to UniProtKB:  A0A7M7KVA6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7M7KVA6
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.604α = 90
b = 112.959β = 98.95
c = 41.817γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary