High resolution crystal structure data of human plasma retinol-binding protein (RBP4) bound to retinol and fatty acids

Retinol is transported in vertebrate plasma bound to a protein called retinol-binding protein (RBP4) so far believed to be specific for the vitamin. When the protein is saturated with retinol it binds tightly to another plasma protein, transthyretin while when not saturated with retinol it does not bind to TTR (Goodman, 1984). The X-ray structures of human RBP4, holo and devoid of retinol in its binding site are known to resolutions of 2.0 and 2.5 Å (Cowan et al., 1990; Zanotti et al., 1993) [2], [3]. We have shown that RBP4 is not specific for retinol but it is also found in plasma, urine and amniotic fluid bound to fatty acids. Here we present 1.5 Å resolution crystal data on human plasma retinol-binding protein bound to retinol and fatty acids. These are the highest resolution data available in the Protein Data Bank for this protein. For further details and experimental findings please refer to the article “ Human plasma retinol-binding protein (RBP4) is also a fatty acid-binding protein” (Perduca et al., 2018) [4].


a b s t r a c t
Retinol is transported in vertebrate plasma bound to a protein called retinol-binding protein (RBP4) so far believed to be specific for the vitamin. When the protein is saturated with retinol it binds tightly to another plasma protein, transthyretin while when not saturated with retinol it does not bind to TTR (Goodman, 1984). The X-ray structures of human RBP4, holo and devoid of retinol in its binding site are known to resolutions of 2.0 and 2.5 Å (Cowan et al., 1990;Zanotti et al., 1993) [2,3]. We have shown that RBP4 is not specific for retinol but it is also found in plasma, urine and amniotic fluid bound to fatty acids. Here we present 1.5 Å resolution crystal data on human plasma retinol-binding protein bound to retinol and fatty acids. These are the highest resolution data available in the Protein Data Bank for this protein.
For further details and experimental findings please refer to the article " Human plasma retinol-binding protein (RBP4) is also a fatty acid-binding protein" (Perduca et  Value of the data.
The extension of the resolution limit of RBP4 permitted the removal of several ambiguities in the models of the holo protein available at lower resolution [2,3]. More important was the identification of a heretofore unidentified ligand in the binding site of the protein believed to be apo. This second result changes substantially our perception of this protein that has so far been considered to be specific for retinol [1].

Data
The data of this article provides information on the X-ray crystallographic data sets of RBP4 purified from different sources. All these data are accessible at the Protein Data Bank. The

Experimental design, materials and methods
The data listed above were collected on two beamlines at the European Synchrotron Radiation Facility (ESRF) in Grenoble. The diffraction data were collected from crystals cooled to 100 K after brief immersion into a mixture of 80% mother liquor and 20% glycerol. The data were indexed, integrated and reduced using the programs MOSFLM [5] and Scala [6]. The processed data were converted to structure factors using the program TRUNCATE from the CCP4 suite [7]. More details on these data are summarized in Table 1 of the article "Human plasma retinol-binding protein (RBP4) is also a fatty acid-binding protein" [4].
In Table 1 we summarize the largest differences between the models of the same crystal form of RBP4 purified from plasma and solved to resolutions of 2.5 Å [3] and 1.5 Å [4] respectively (PDB accession codes 1BRP and 5NU7). The first column of the table identifies the amino acid and the second the atom where the largest difference was found while the last column gives a description of the electron density quality in the two maps. Third and fourth column record the differences in B factors and the distance between the two positions measured in Angstroms.
In a similar manner, Table 2 compares the models of the same crystal form of RBP4 purified from plasma, not bound to retinol and solved to a resolution of 2.5 Å [3] and 2.0 Å [4]. Table 3 analyses the differences between RBP4 purified from plasma and bound to palmitic acid and retinol.
The shortest distances between RBP4 residues and three ligands, palmitate (Table 4), laurate (Table 5) and retinol (Table 6) are listed in the three tables. The main interactions between RBP4 and retinol and palmitate are represented in Figs. 1 and 2 respectively. Table 7 lists the ligand binding cavities of the two RBP4 populations analyzed, i.e bound to retinol and to fatty acids calculated from the coordinates of the models using the program CASTp [8].  Table 3 Main differences between non-fluorescent and holo RBP4 in the 2.0 and 1.5 Å resolution models (crystal forms 1 & 4 in Table 1 of reference [4]).

RBP4 residue
Atom   Table 4 RBP4 residues in contact with palmitate in Crystal form 6.
Only the shortest distance per residue has been included in the table. The residues in yellow are in contact with all the ligands Table 5 RBP4 residues in contact with laurate in Crystal form 8.
Only the shortest distance per residue has been included in the table. The residues in yellow are in contact with all the ligands Table 6 RBP4 residues in contact with retinol in Crystal form 4.
Only the shortest distance per residue has been included in the table. The residues in yellow are in contact with all the ligands Fig. 1. Gln 98 and other side chains participating in the specific contacts of RBP4 with retinol. A hydrogen bond is indicated with green broken lines, whereas the amino acids that make hydrophobic contacts are only indicated but not represented as ball and stick models.

Acknowledgements
This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Transparency document. Supplementary material
Supplementary data associated with this article can be found in the online version at http://dx.doi. org/10.1016/j.dib.2018.03.112. Fig. 2. Interaction of Lys 29 , Phe 36 and Leu 37 and other side chains participating in the specific contacts of RBP4 with palmitic acid. Hydrogen bonds are indicated with green broken lines, whereas the amino acids that make hydrophobic contacts are only indicated but not represented as ball and stick models. The cavity volume computations were done with the program CASTp [8]