7NYJ image
Deposition Date 2021-03-22
Release Date 2021-07-07
Last Version Date 2024-10-09
Entry Detail
PDB ID:
7NYJ
Title:
Structure of OBP1 from Varroa destructor, form P3<2>21
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.81 Å
R-Value Free:
0.22
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 32 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Odorant Binding Protein 1 from Varoa destructor, form P3<2>21
Chain IDs:A
Chain Length:147
Number of Molecules:1
Biological Source:Varroa destructor
Primary Citation
A new non-classical fold of varroa odorant-binding proteins reveals a wide open internal cavity.
Sci Rep 11 13172 13172 (2021)
PMID: 34162975 DOI: 10.1038/s41598-021-92604-2

Abstact

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.

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