Data for the homology modelling of the red pigment-concentrating hormone receptor (Dappu-RPCHR) of the crustacean Daphnia pulex, and docking of its cognate agonist (Dappu-RPCH)

The data presented in this article are related to the publication “Interaction of the red pigment-concentrating hormone of the crustacean Daphnia pulex, with its cognate receptor, Dappu-RPCHR: A nuclear magnetic resonance and modeling study” (Jackson et al., 2017) [1]. This article contains the data for homology modeling of the red pigment-concentrating hormone (RPCH) receptor of the water flea, Daphnia pulex (Dappu-RPCHR), which was constructed from its primary sequence. This is the first 3D model of a crustacean G-protein coupled receptor. Docking of the agonist, pGlu-Val-Asn-Phe-Ser-Thr-Ser-Trp amide (Dappu-RPCH), was used to find a binding pocket on the receptor and compared to the binding pocket of the adipokinetic hormone (AKH) receptor from the malaria mosquito. Data for the receptor, with and without loop refinement, together with the docked agonist, are presented.


Value of the Data
This is the first model of a crustacean G-protein coupled receptor This is the first comparison of homology modelling of a crustacean GPCR and an insect GPCR. This data allows others to extend the study to other agonists and crustacean GPCRs. This is the first study of hormone docking to a crustacean receptor. The final docked position was very similar, but not identical, to other GPCR/ligand complexes.

Data
The raw data for the Dappu-RPCH receptor [1], with and without loop refinement, together with the docked agonist are given in protein database (pdb) format as supplementary data. Fig. 1 shows the primary sequence of the receptor, which was obtained from Anders [7]. This sequence compares closely to the Genbank sequence (EU503126.1) with 97.2% sequence identity. The GPCRpred server predicts that this receptor belongs to the CLASS A, rhodopsin superfamily, of G-protein coupled receptors. Fig. 2 shows the MEMSAT-SVM and MEMSAT3 [8] analysis of the primary sequence data of Dappu-RPCHR. Seven transmembrane helices are predicted with a short N-terminus and long C-terminus.        4 shows a Ramachandran plot of the Dappu-RPCHR model. Of the model residues, 89.2% occupy the core regions (red), 7.5% occupy allowed regions (yellow), 2.6% occupy generously allowed regions (light yellow), and 0.7% occupy disallowed regions (white). Fig. 5 shows the evaluation of the Dappu-RPCHR model by the Verify3D program [9]. Residues with positive compatibility score show that the model is reasonably folded. Fig. 6 shows the molecular dynamics of the agonist, Dappu-RPCH in water. The figure shows the molecule jumping between its two major clusters. Fig. 7 shows an overlay of the receptor Dappu-RPCHR (cyan) and the AKH receptor (green) (Anoga-HrTHR) of the malaria mosquito, A. gambiae [10]. Fig. 7(B) shows an overlay of their respective agonists, Dappu-RPCH and Anoga-HrTH.
Since the β-adrenergic receptor (β2AR) was used as the template during the construction of Dappu-RPCHR it is interesting to compare the binding of agonists to these two receptors. Carazolol is a high affinity agonist of β2AR. Fig. 8 shows a comparison of the predicted binding sites for Dappu-RPCH in Dappu-RPCHR and carazolol in β2AR.
The GPCR-ModSim Web server (http://gpcr-modsim.org/) [13] was used for template selection and preliminary sequence alignment. Modeler 9v7 [2] was used to construct 3D models of the receptor. The quality of the constructed model was evaluated for its internal consistency and reliability using a Ramachandran plot and checking the quality of non-bonded atom interactions by ERRAT [6]. Autodock Vina

Acknowledgments
This work is based on the research supported in part by the National Research Foundation of South Africa (Grant numbers 93450 and 85466 to GEJ and 85768 to GG) and the University of Cape Town Research Committee (453509).

Transparency document. Supporting information
Transparency data associated with this article can be found in the online version at http://dx.doi. org/10.1016/j.dib.2017.10.045.