N-terminal Sequencing and Mass Analyses—The identity and integrity of the purified protein were assessed by N-terminal amino acid sequencing by Edman degradation and various mass spectrometric analyses, including MALDI-TOF/MS, MALDI-TOF/TOF-MS/MS, nano-liquid chromatographyquadrapole TOF-MS/MS, and high performance liquid chromatography-electrospray ionization-iontrap-MS/MS as described in the supplemental materials (14 (link)).
Crystallization—Crystals were grown by the hanging-drop vapor diffusion method. One microliter of protein sample (10 mg/ml) in a solution of 10 m
Structure Determination and Refinement—X-ray diffraction data were collected at 100 K on beam line BL45XU at SPring-8. Data were reduced using the program HKL2000 (15 ). The structure was determined by molecular replacement with the program MOLREP in the CCP4 program suite (16 (link)) using a monomer of the trigonal crystal structure of the bovine rhodopsin (PDB code: 1GZM) (17 ) as a search model. Refinement and model building were performed iteratively with the programs CNS (18 (link)), REFMAC5 in CCP4 (16 (link)), and O (19 (link)). During refinement, we used grouped, unrestrained B-factor refinement with a single group for the entire molecule. All refinements were carried out with 10% of the reflections for cross validation. Despite the low resolution data and the low sequence homology between squid and bovine rhodopsins (24%), the structure was well refined thanks to the structural similarity of the transmembrane helices and the positions for a disulfide bridge, an 11-cis-retinal chromophore in the Schiff base linkage, and the conserved residues. B-factor sharpening was used to generate detailed maps using the CNS program with Bsharp values ranging from –50 to –150 Å2 (20 ). Data collection and refinement statistics are shown in
Wavelength (Å) | 0.97950 |
Resolution (Å) | 43.2-3.7 |
Measured reflections | 43,571 |
Unique reflections | 6,680 |
Completeness (%) | 93.3 (74.3) |
Rmerge (%) | 6.4 (77.5) |
Space group | C2221 |
Unit cell (Å) | a = 84.3, b = 108.7, c = 142.2 |
Resolution (Å) | 43.2-3.7 |
Reflections used | 6,647 |
Rwork/Rfree (%) | 30.2/33.0 (41.4/43.2) |
r.m.s. | |
bond (Å) | 0.014 |
angle (°) | 2.01 |
Ramachandran statistics | |
Most favored region (%) | 70.4 |
Additional allowed region (%) | 27.1 |
Generously allowed region (%) | 2.1 |
Disallowed region (%) | 0.3 |
Values in parentheses are for the highest-resolution shell (3.83-3.70 Å).
Rmerge = ∑i|I(h)i — 〈I(h)〉|/∑i|I(h)i|, where 〈I(h)〉 is the mean intensity of equivalent reflections.
The last shell Rmerge is rather high as a result of strong anisotropy.
Rwork = ∑|Fo — Fc|/∑|Fo|, where Fo and Fc are the observed and calculated structure factor amplitudes, respectively.
Rfree = ∑|Fo — Fc|/∑|Fo|, calculated using a test data set, 10% of total data randomly selected from the observed reflections.
r.m.s., root mean square.