The phytohormone abscisic acid (ABA) mediates the adaptation of plants to environmental stresses such as drought and regulates developmental signals such as seed maturation. Within plants, the PYR/PYL/RCAR family of START proteins receives ABA to inhibit the phosphatase activity of the group-A protein phosphatases 2C (PP2Cs), which are major negative regulators in ABA signalling. Here we present the crystal structures of the ABA receptor PYL1 bound with (+)-ABA, and the complex formed by the further binding of (+)-ABA-bound PYL1 with the PP2C protein ABI1. PYL1 binds (+)-ABA using the START-protein-specific ligand-binding site, thereby forming a hydrophobic pocket on the surface of the closed lid. (+)-ABA-bound PYL1 tightly interacts with a PP2C domain of ABI1 by using the hydrophobic pocket to cover the active site of ABI1 like a plug. Our results reveal the structural basis of the mechanism of (+)-ABA-dependent inhibition of ABI1 by PYL1 in ABA signalling.

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Data deposits

Structure coordinates and structural factors are deposited in the Protein Data Bank under accession numbers 3JRS (PYL1–(+)-ABA) and 3JRQ (PYL1–(+)-ABA–ABI1).


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The synchrotron-radiation experiments were performed at BL5A in the Photon Factory (2008S2-001). This work was supported by the Targeted Proteins Research Program (TPRP) of the Ministry of Education, Culture, Sports, Science, and Technology, Japan. We thank Y. Sakaguchi (DKSH Japan K.K.) and Y. Asami (TA Instruments Japan Inc.) for the ITC measurements and T. Mitani (GE Healthcare Japan Corp.) for the SPR experiments.

Author Contributions M. Tanokura conceived and designed the project. K.-i.M., T.M., Y.S. and K. Kubota performed the construct design, subcloning, protein expression, purification, crystallization, structure determination and all biochemical assays. H.-J.K., A.A., Y.M, M. Takahashi and Y.Z. also assisted in the subcloning, protein expression, purification and crystallization. Y.F., T.Y. and K. Kodaira performed the cloning. K.-i.M., T.M., Y.S, K. Kubota, K.Y.-S. and M. Tanokura wrote the manuscript and M. Tanokura edited the manuscript.

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Author notes

    • Ken-ichi Miyazono
    • , Takuya Miyakawa
    • , Yoriko Sawano
    •  & Keiko Kubota

    These authors contributed equally to this work.


  1. Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan

    • Ken-ichi Miyazono
    • , Takuya Miyakawa
    • , Yoriko Sawano
    • , Keiko Kubota
    • , Hee-Jin Kang
    • , Atsuko Asano
    • , Yumiko Miyauchi
    • , Mihoko Takahashi
    • , Yuehua Zhi
    •  & Masaru Tanokura
  2. Biological Resources Division, Japan International Research Center for Agricultural Sciences, Ibaraki 305-8686, Japan

    • Yasunari Fujita
    • , Takuya Yoshida
    • , Ken-Suke Kodaira
    •  & Kazuko Yamaguchi-Shinozaki
  3. Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan

    • Takuya Yoshida
    • , Ken-Suke Kodaira
    •  & Kazuko Yamaguchi-Shinozaki


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Correspondence to Masaru Tanokura.

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    Supplementary Information

    This file contains Supplementary Results and Discussion, Supplementary References, Supplementary Tables 1 - 2 and Supplementary Figures 1 - 8 with Legends. This file was replaced on 24 December 2009 to correct minor errors in Supplementary Table 1.

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