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Crystal structure of squid rhodopsin

Nature volume 453, pages 363–367 (2008)Cite this article

Abstract

Invertebrate phototransduction uses an inositol-1,4,5-trisphosphate signalling cascade in which photoactivated rhodopsin stimulates a Gq-type G protein, that is, a class of G protein that stimulates membrane-bound phospholipase Cβ. The same cascade is used by many G-protein-coupled receptors, indicating that invertebrate rhodopsin is a prototypical member. Here we report the crystal structure of squid (Todarodes pacificus) rhodopsin at 2.5 Å resolution. Among seven transmembrane α-helices, helices V and VI extend into the cytoplasmic medium and, together with two cytoplasmic helices, they form a rigid protrusion from the membrane surface. This peculiar structure, which is not seen in bovine rhodopsin, seems to be crucial for the recognition of Gq-type G proteins. The retinal Schiff base forms a hydrogen bond to Asn 87 or Tyr 111; it is far from the putative counterion Glu 180. In the crystal, a tight association is formed between the amino-terminal polypeptides of neighbouring monomers; this intermembrane dimerization may be responsible for the organization of hexagonally packed microvillar membranes in the photoreceptor rhabdom.

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Figure 1: Schematic diagram of the topology of squid rhodopsin.
Figure 2: Crystal structure of C-terminally truncated squid rhodopsin.
Figure 3: Structural comparisons between squid rhodopsin and bovine rhodopsin.
Figure 4: Retinal-binding pocket and interhelical cavity.
Figure 5: Cytoplasmic view of C-terminally truncated squid rhodopsin.

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Accession codes

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Protein Data Bank

Data deposits

The coordinates have been deposited in the Protein Data Bank under accession number 2z73.

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Acknowledgements

This work was supported by Grant-in-Aids from the Ministry of Education, Science and Culture of Japan and partly by the National Project on Protein Structural and Functional Analyses.

Author Contributions T.K. and M.M. designed the project. M.M. performed all experiments. T.K. assisted in data collection and structure determination. T.K. and M.M. jointly wrote the manuscript.

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Authors and Affiliations

  1. Department of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan

    Midori Murakami & Tsutomu Kouyama

  2. RIKEN Harima Institute/SPring-8, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan,

    Tsutomu Kouyama

Authors
  1. Midori Murakami
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  2. Tsutomu Kouyama
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Corresponding author

Correspondence to Tsutomu Kouyama.

Supplementary information

Supplementary information

The file contains Supplementary Tables S1-S2, Figure S1 and Legends. Supplementary Table S1 includes X-ray data collection and refinement statistics. Supplementary Table S2 shows the distances to the closest atoms of all amino acids around the retinal. Supplementary Figure S1 shows the multiple sequence alignment of squid and bovine rhodopsins. (PDF 371 kb)

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Murakami, M., Kouyama, T. Crystal structure of squid rhodopsin. Nature 453, 363–367 (2008). https://doi.org/10.1038/nature06925

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