KEKユーザーとの共同研究の成果

• ◾️ Effect of alkali metal cations on the unilamellar vesicle of a squalene bearing 18-crown-6.
  Linh, T.N., Arimura, T., Tominaga, K., Isoda, H., Kawasaki, M., and Adachi, N.
  ACS Omega Online ahead of print (2023).
• ◾️ Uphill energy transfer mechanism for photosynthesis in an Antarctic alga.
  Kosugi, M., Kawasaki, M., Shibata, Y., Hara, K., Takaichi, S., Moriya, T., Adachi, N., Kamei, Y., Kashino, Y., Kudoh, S., Koike, H. and Senda, T.
  Nature Commun. 14, 730 (2023). EMDB-35080@3.13Å (PDB:8HW1) (EMPIAR-)
• ◾️ Reversible Assembly of an Artificial Protein Nanocage Using Alkaline Earth Metal Ions.
  Ohara, N., Kawakami, N., Arai, R., Adachi, N., Moriya, T., Kawasaki, M., and Miyamoto, K.
  J. Am. Chem. Soc. Online ahead of print (2022). EMDB-33289@3.96Å (PDB:7xm1) (EMPIAR-)
• ◾️ Structural basis for activation of DNMT1.
  Kikuchi, A., Onoda, H., Yamaguchi, K., Kori, S., Matsuzawa, S., Chiba, Y., Tanimoto, S., Yoshimi, S., Sato, H., Yamagata, A., Shirouzu, M., Adachi, N., Sharif, J., Koseki, H., Nishiyama, A., Nakanishi, M., Defossez, P.A., and Arita, K.
  Nature Commun. 13, 7130 (2022). EMDB-33200@2.52Å @TokyoU-Titan (PDB:7xi9) EMDB-33201@2.23Å @TokyoU-Titan (PDB:7xib)
• ◾️ Structural bases for aspartate recognition and polymerization efficiency of cyanobacterial cyanophycin synthetase.
  Miyakawa, T., Yang, J., Kawasaki, M., Adachi, N., Fujii, A., Miyauchi, Y., Muramatsu, T., Moriya, T., Senda, T., and Tanokura, M.
  Nature Commun. 13, 5097 (2022). EMDB-32381@2.91Å (PDB:7wac) (EMPIAR-) EMDB-32382@2.96Å (PDB:7wad) (EMPIAR-) EMDB-32383@2.64Å @TokyoU-Titan (PDB:7wae) EMDB-32384@2.52Å @TokyoU-Titan (PDB:7waf)
• ◾️ Core fucose-specific Pholiota squarrosa lectin (PhoSL) as a potent broad-spectrum inhibitor of SARS-CoV-2 infection.
  Yamasaki, K., Adachi, N., Ngwe Tun, M.M., Ikeda, A., Moriya, T., Kawasaki, M., Yamasaki, T., Kubota, T., Nagashima, I., Shimizu, H., Tateno, H., and Morita, K.
  FEBS J. in press (2022).
• ◾️ Discovery of non-squalene triterpenes.
  Tao, H., Lauterbach, L., Bian, G., Chen, R., Hou, A., Mori, T., Cheng, S., Hu, B., Lu, L., Mu, X., Li, M., Adachi, N., Kawasaki, M., Moriya, T., Senda, T., Wang, X., Deng, Z., Abe, I., Dickschat J.S., and Liu, T.
  Nature 606, 414-419 (2022). EMDB-32531@3.17Å (PDB:7wij) (EMPIAR-11409)
  EMDB-32532@4.00Å (PDB:----) (EMPIAR-11409)
• ◾️ Structural basis of the strict specificity of a bacterial GH31 α-1,3-glucosidase for nigerooligosaccharides.
  Ikegaya, M., Moriya, T., Adachi, N., Kawasaki, M., Park, E.Y., and Miyazaki, T.
  J. Biol. Chem. 298, 101827 (2022). EMDB-32571@2.73Å (PDB:7wlg) (EMPIAR-11171)
• ◾️ Structural and Functional Analyses of the Tridomain-Nonribosomal Peptide Synthetase FmoA3 for 4-Methyloxazoline Ring Formation
  2021, Vol. 133, Pages 14675-14683
  EMDB: EMD-30440 (PDB: Not available) (EMPIAR: EMPIAR-11059)
  
• ◾️ C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes.
  Mori, T., Kumano, T., He, H., Watanabe, S., Senda, M., Moriya, T., Adachi, N., Hori, S., Terashita, Y., Kawasaki, M., Hashimoto, Y., Awakawa, T., Senda, T., Abe, I., and Kobayashi, M.
  Nature Commun. 12, 6294 (2021). EMDB-30808@2.85Å (PDB:7drd) (EMPIAR-11124)
  EMDB-30809@2.54Å (PDB:7dre) (EMPIAR-11138)
• ◾️ Non-conventional octameric structure of C-phycocyanin.
  Minato, T., Teramoto, T., Adachi, N., Hung, N.K., Yamada, K., Kawasaki, M., Akutsu, M., Moriya, T., Senda, T., Ogo, S., Kakuta, Y., and Yoon, K.S.
  Commun. Biol. 4, 1238 (2021). EMDB-31090@3.06Å (PDB:7eh8) (EMPIAR-11079)
  EMDB-31089@3.71Å (PDB:7eh7) (EMPIAR-11079)
• ◾️ Cryo-EM structure of the nucleosome core particle containing Giardia lamblia histones.
  Sato, S., Takizawa, Y., Hoshikawa, F., Dacher, M., Tanaka, H., Tachiwana, H., Kujirai, T., Iikura, Y., Ho, C.H., Adachi, N., Patwal, I., Flaus, A., and Kurumizaka, H.
  Nucleic Acids Res. 49, 8934-8946 (2021). EMDB-30591@3.57Å @TokyoU-Titan (PDB:7d69)
• ◾️ Minimal protein-only RNase P structure reveals insights into tRNA precursor recognition and catalysis.
  Teramoto, T., Koyasu, T., Adachi, N., Kawasaki, M., Moriya, T., Numata, T., Senda, T., and Kakuta, Y.
  J. Biol. Chem. 297, 101028 (2021). EMDB-31432@3.62Å (PDB:7f3e) (EMPIAR-11072)
• ◾️ 2.85 and 2.99 Å resolution structures of 110 kDa nitrite reductase determined by 200 kV cryogenic electron microscopy.
  Adachi, N., Yamaguchi, T., Moriya, T., Kawasaki, M., Koiwai, K., Shinoda, A., Yamada, Y., Yumoto, F., Kohzuma, T., and Senda, T.
  J. Struct. Biol. 213, 107768 (2021). EMDB-0730@2.99Å (PDB:6knf) (EMPIAR-10580)
  EMDB-0731@2.85Å (PDB:6kng) (EMPIAR-10581)
• ◾️ DNA polymerase D temporarily connects primase to the CMG-like helicase before interacting with proliferating cell nuclear antigen.
  Oki, K., Yamagami, T., Nagata, M., Mayanagi, K., Shirai, T., Adachi, N., Numata, T., Ishino, S., and Ishino Y.
  Nucleic Acids Res. 49, 4599-4612 (2021). EMDB-30937@7.1Å (EMPIAR-11061)
• ◾️ Structural and functional analyses of the tridomain-nonribosomal peptide synthetase FmoA3 for 4-methyloxazoline ring formation.
  Katsuyama, Y., Sone, K., Harada, A., Kawai, S., Urano, N., Adachi, N., Moriya, T., Kawasaki, M., Shin-Ya, K., Senda, T., and Ohnishi, Y.
  Angew. Chem. 60, 14554-14562 (2021). EMDB-30440@3.55Å (EMPIAR-11059)
• ◾️ Cryo-EM structure of K+-bound hERG channel complexed with the blocker astemizole.
  Asai, T., Adachi, N., Moriya, T., Oki, H., Maru, T., Kawasaki, M., Suzuki, K., Chen, S., Ishii, R., Yonemori, K., Igaki, S., Yasuda, S., Ogasawara, S., Senda, T., and Murata, T.
  Structure 29, 203-212 (2021). EMDB-30412@3.90Å (PDB:7cn0) (EMPIAR-10628)
  EMDB-30413@3.70Å (PDB:7cn1) (EMPIAR-10629)
• ◾️ Structural analysis reveals TLR7 dynamics underlying antagonism.
  Tojo, S., Zhang, Z., Matsui, H., Tahara, M., Ikeguchi, M., Kochi, M., Kamada, M., Shigematsu, H., Tsutsumi, A., Adachi, N., Shibata, T., Yamamoto, M., Kikkawa, M., Senda, T., Isobe, Y., Ohto, U., and Shimizu, T.
  Nature Commun. 11, 5204 (2020). EMDB-30002@2.8Å @TokyoU-Titan (PDB:6lw1)
• ◾️ Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase from Sulfurisphaera tokodaii.
  Sato, Y., Yabuki, T., Adachi, N., Moriya, T., Arakawa, T., Kawasaki, M., Yamada, C., Senda, T., Fushinobu, S., and Wakagi, T.
  J. Struct. Biol. X. 4, 100030 (2020). EMDB-30073@2.24Å (PDB:6m3x) (EMPIAR-10546)
  EMDB-30362@2.05Å (EMPIAR-10546)

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KEKユーザーによる施設利用の成果

• ◾️ Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases.
  Nishida, Y., Yanagisawa, S., Morita, R., Shigematsu, H., Shinzawa-Itoh, K., Yuki, H., Ogasawara, S., Shimuta, K., Iwamoto, T., Nakabayashi, C., Matsumura, W., Kato, H., Gopalasingam, C., Nagao, T., Qaqorh, T., Takahashi, Y., Yamazaki, S., Kamiya, K., Harada, R., Mizuno, N., Takahashi, H., Akeda, Y., Ohnishi, M., Ishii, Y., Kumasaka, T., Murata, T., Muramoto, K., Tosha, T., Shiro, Y., Honma, T., Shigeta, Y., Kubo, M., Takashima, S., and Shintani, Y.
  Nature Commun. 13, 7591 (2022).
• ◾️ Design and lyophilization of lipid nanoparticles for mRNA vaccine and its robust immune response in mice and nonhuman primates.
  Suzuki, Y., Miyazaki, T., Muto, H., Kubara, K., Mukai, Y., Watari, R., Sato, S., Kondo, K., Tsukumo, S.I., Yasutomo, K., Ito, M., and Tsukahara, K.
  Mol. Ther. Nucleic Acids 30, 226-240 (2022).
• ◾️ Syntheses and aggregation properties of new squalene receptors bearing open chain ligands.
  Linh, T.N., Arimura, T., Tominaga, K., Kigoshi, H., and Isoda, H.
  Supramolecular Chemistry 33, 194-201 (2021).

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KEKメンバーによる高度化研究の成果

• ◾️ Size matters: optimal mask diameter and box size for single-particle cryogenic electron microscopy.
  Moriya, T., Adachi, N., Kawasaki, M., Yamada, Y., Shinoda, A., Koiwai, K., Yumoto, F., and Senda, T.
  bioRxiv (2020).