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Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 Å resolution

Nature volume 405, pages 647–655 (2000)Cite this article

Abstract

Calcium ATPase is a member of the P-type ATPases that transport ions across the membrane against a concentration gradient. Here we have solved the crystal structure of the calcium ATPase of skeletal muscle sarcoplasmic reticulum (SERCA1a) at 2.6 Å resolution with two calcium ions bound in the transmembrane domain, which comprises ten α-helices. The two calcium ions are located side by side and are surrounded by four transmembrane helices, two of which are unwound for efficient coordination geometry. The cytoplasmic region consists of three well separated domains, with the phosphorylation site in the central catalytic domain and the adenosine-binding site on another domain. The phosphorylation domain has the same fold as haloacid dehalogenase. Comparison with a low-resolution electron density map of the enzyme in the absence of calcium and with biochemical data suggests that large domain movements take place during active transport.

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Figure 1: Crystal packing of Ca2+-ATPase in the plate-like crystals.
Figure 2: Architecture of the sarcoplasmic reticulum Ca2+-ATPase. α-Helices are represented by cylinders and β-strands by arrows, as recognized by DSSP46.
Figure 3: The arrangement of transmembrane helices (a), an enlarged view of a part of M5 helix (b) and water accessible cavities on the cytoplasmic surface (in stereo, c).
Figure 4: Details of the transmembrane Ca2+-binding sites.
Figure 5: Architecture of the phosphorylation domain (P in Fig. 2) of Ca2+-ATPase (a) and the catalytic core domain of L-2-haloacid dehalogenase (HAD23, b).
Figure 6: Binding of TNP-AMP to Ca2+-ATPase.
Figure 7: Fitting the atomic model obtained for the Ca2+-bound state (arrows and cylinders) to an 8 Å resolution map (blue net) obtained from tubular crystals formed in the absence of Ca2+ and presence of decavanadate and dansyl-thapsigargin13.
Figure 8: Coupling of the phosphorylation domain and the transmembrane domain by the loop (L67) connecting helices M6 and M7.

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Acknowledgements

We thank S. Adachi, N. Kamiya (Riken) and M. Kawamoto (JASRI) for their help in data taking at SPring-8, and K. Tani for computations. We acknowledge that very first crystals for X-ray were made by H. Mukai. This work was supported in part by grants-in-aid from the Ministry of Culture, Education, Science and Sports of Japan and from CRESTO (to C.T. and M.N.) and also by Toray Science Foundation (C.T.). This paper is dedicated to S. Ebashi, a founder of Ca2+-ATPase field and the father of the calcium theory.

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Authors and Affiliations

  1. Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan

    Chikashi Toyoshima, Masayoshi Nakasako, Hiromi Nomura & Haruo Ogawa

  2. The Harima Institute, The Institute of Physical and Chemical Research, Sayo-gun, Hyo-go, 679-5143, Japan

    Chikashi Toyoshima & Masayoshi Nakasako

  3. PRESTO, Japan Science and Technology Corporation, Kawaguchi, 332-0012, Japan

    Masayoshi Nakasako

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Correspondence to Chikashi Toyoshima.

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Toyoshima, C., Nakasako, M., Nomura, H. et al. Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 Å resolution. Nature 405, 647–655 (2000). https://doi.org/10.1038/35015017

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