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Shimada Atsushi Last modified date:2022.07.05

Associate Professor / Division of Structural Biology
Medical Institute of Bioregulation

Graduate School

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Division of Structural Biology, Medical Institute of Bioregulation .
Academic Degree
Country of degree conferring institution (Overseas)
Field of Specialization
structural biology, biochemistry, cell biology
ORCID(Open Researcher and Contributor ID)
Total Priod of education and research career in the foreign country
Outline Activities
Cell biological phenomena, such as cell migration and endocytosis, are dynamic processes accompanied with membrane and/or actin cytoskeletal remodeling. These processes are regulated by cellular signaling pathways, which link extracellular signals to corresponding morphological changes of the cell. A number of proteins with various functions are involved in these pathways, which include those with membrane remodeling and/or actin remodeling activities. However, the detailed functions of many of these proteins at atomic resolution are still not fully understood. To reveal novel mechanisms exerted by these proteins, which support the maintenance of the activities of eukaryotic cells, structural and functional analyses are being performed using mainly X-ray crystallography, electron microscopy, and biochemical techniques, such as isothermal titration calorimetry. Cell biological analyses to test hypotheses derived from structural and functional analyses are also being performed in collaboration with other groups.
Research Interests
  • Development of a novel method for the structural analysis of membrane proteins
    keyword : membrane protein
  • Structural and functional analyses of phagocytosis-related proteins
    keyword : Phagocytosis, GAS7, F-BAR domain
  • Crystallography of the complex between a novel plant actin-binding domain and actin
    keyword : plant, actin, FH2 domain
  • Structural biology of oligosaccharyltransferases
    keyword : oligosaccharyltransferase, N-glycosylation
  • Structural basis of vesicle formation in endocytosis
    keyword : X-ray crystallography, endocytosis, BAR domain, EFC/F-BAR domain
Current and Past Project
  • Structural and functional studies of a protein family involved in ER-Golgi and Golgi-endosome trafficking and regulation of ER-mitochondria contact sites.
Academic Activities
1. Atsushi Shimada and Shigeyuki Yokoyama, Crystal structure of the EFC/F-BAR domain -mechanism of membrane invagination in endocytosis-, SPring-8 Research Frontiers 2007, 2008.07.
1. Hanawa-Suetsugu K, Itoh Y, Ab Fatah M, Nishimura T, Takemura K, Takeshita K, Kubota S, Miyazaki N, Wan Mohamad Noor WNI, Inaba T, Nguyen NTH, Hamada-Nakahara S, Oono-Yakura K, Tachikawa M, Iwasaki K, Kohda D, Yamamoto M, Kitao A, Shimada A, Suetsugu S., Phagocytosis is mediated by two-dimensional assemblies of the F-BAR protein GAS7, Nature Communications, 10.1038/s41467-019-12738-w, 10, 4763, 2019.10, Phagocytosis is a cellular process for internalization of micron-sized large particles including pathogens. The Bin-Amphiphysin-Rvs167 (BAR) domain proteins, including the FCH-BAR (F-BAR) domain proteins, impose specific morphologies on lipid membranes. Most BAR domain proteins are thought to form membrane invaginations or protrusions by assembling into helical submicron-diameter filaments, such as on clathrin-coated pits, caveolae, and filopodia. However, the mechanism by which BAR domain proteins assemble into micron-scale phagocytic cups was unclear. Here, we show that the two-dimensional sheet-like assembly of Growth Arrest-Specific 7 (GAS7) plays a critical role in phagocytic cup formation in macrophages. GAS7 has the F-BAR domain that possesses unique hydrophilic loops for two-dimensional sheet formation on flat membranes. Super-resolution microscopy reveals the similar assemblies of GAS7 on phagocytic cups and liposomes. The mutations of the loops abolishes both the membrane localization of GAS7 and phagocytosis. Thus, the sheet-like assembly of GAS7 plays a significant role in phagocytosis..
2. Atsushi Shimada, Atsuko Yamaguchi, Daisuke Kohda, Structural basis for the recognition of two consecutive mutually interacting DPF motifs by the SGIP1 μ homology domain., Sci. Rep., 29, 6, 19565, 2016.01.
3. Shimada, A., Takano, K., Shirouzu, M., Hanawa-Suetsugu, K., Terada, T., Toyooka, K., Umehara, T., Yamamoto, M., Yokoyama, S. and Suetsugu, S., Mapping of the basic amino-acid residues responsible for tabulation and cellular protrusion by EFC/F-BAR domain of pacsin2/Syndapin II, FEBS Lett., 584, 6, 1111-1118, 2010.03.
4. Shimada, A., Niwa, H., Tsujita, K., Suetsugu, S., Nitta, K., Hanawa-Suetsugu, K., Akasaka, R., Nishino, Y., Toyama, M., Chen, L., Liu, Z.J., Wang, B.C., Yamamoto, M., Terada, T., Miyazawa, A., Tanaka, A., Sugano, S., Shirouzu, M., Nagayama, K., Takenawa, T. and Yokoyama, S. , Curved EFC/F-BAR domain dimers are joined end to end into a filament for membrane invagination in endocytosis
, Cell, 129, 4, 761-772, 2007.05.
5. Shimada, A., Nyitrai, M., Vetter, I.R., Kuhlmann, D., Bugyi, B., Narumiya, S., Geeves, M.A. and Wittinghofer, A., The core FH2 domain of diaphanous-related formins is an elongated actin binding protein that inhibits polymerization
, Mol. Cell, 13, 4, 511-522, 2004.02.
6. Shimada, A., Nureki, O., Goto, M., Takahashi, S. and Yokoyama S, Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase
, Proc. Natl. Acad. Sci. USA, 98, 24, 13537-13542, 2001.11.
7. Sekine, S., Nureki, O., Shimada, A., Vassylyev, D.G. and Yokoyama S, Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase, Nat. Struct. Biol., 8, 3, 203-206, 2001.03.
8. Fukai, S., Nureki, O., Sekine, S., Shimada, A., Tao, J., Vassylyev, D.G. and Yokoyama, S., Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase, Cell, 103, 5, 793-803, 2000.11.
9. Nureki, O., Vassylyev, D.G., Tateno, M., Shimada, A., Nakama, T., Fukai, S., Konno, M., Hendrickson, T.L., Schimmel, P. and Yokoyama, S., Enzyme structure with two catalytic sites for double-sieve selection of substrate, Science, 280, 5363, 578-582, 1998.04.
1. 嶋田 睦, エンドサイトーシス関連細胞質タンパク質の構造から迫るクラスリン重合機構 (Insights into clathrin assembly from the structures of cytosolic endocytic proteins), 第55回 日本生物物理学会年会, 2017.09.
2. 嶋田 睦, 山口 淳子, 神田 大輔, Structural basis for the recognition of two consecutive mutually interacting DPF motifs by the SGIP1 μ homology domain and its implications for the mechanism of affinity enhancement by the increase in the number of consecutive DPF motifs, The 42nd Naito Conference, “In the Vanguard of Structural Biology: Revolutionizing Life Sciences”, 2016.10.
3. Atsuko Yamaguchi, Daisuke Kohda, Atsushi Shimada, Structural basis for the recognition of tandem DPF motifs by the SGIP1 μ homology domain, International Symposium between Kyushu University Post-Global Centers of Excellence Program and School of Biomedical Sciences, Monash University, 2014.02.
Membership in Academic Society
  • Japanese Biochemical Society
  • Protein Science Society of Japan
  • The Molecular Biology Society of Japan
  • The Biophysical Society of Japan
Educational Activities
Teaching undergraduate and graduate students research skills including biochemical and structural biological techniques.