Development of single particle electron microscopy

2009 Fiscal Year Final Research Report

• Project/Area Number: 16087210
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: National Institute of Advanced Industrial Science and Technology
• Principal Investigator: SATO Chikara National Institute of Advanced Industrial Science and Technology, 脳神経情報研究部門, 研究グループ長 (00357146)
• Co-Investigator(Kenkyū-buntansha): KAWATA Masaaki 独立行政法人産業技術総合研究所, 情報技術研究部門, 主任研究員 (20356843) ; OGURA Toshihiko 独立行政法人産業技術総合研究所, 脳神経情報研究部門, 主任研究員 (70371028) ; MIO Kazuhiro 独立行政法人産業技術総合研究所, バイオメディシナル情報センター, 主任研究員 (40470041)
• Project Period (FY): 2004 – 2009
• Keywords: タンパク質 / 3次元構造決定 / 電子顕微鏡 / ナノテクノロジー / 画像情報処理 / ニューラルネット / グリッドコンピューティング / クライオ電顕

Research Abstract

Single particle 3D reconstruction is a method produced bycombining biochemistry, electron microscopy and image analysis. To improve theresolution and automation of single particle reconstruction (SPR), we have introducedsimulated annealing (SA) to SPR, and developed it. These methods were first applied to theion channels, such as TRPC3, TRPM2 and Orai1, then to CFTR ion pump Prestin, carcinogenesis related keap1, and further to Alzheimer disease related γ-secretase.

Research Products

• [Journal Article] Keap1 is a forked-stem dimer struct ure with two large spheres enclosin g the intervening, double glycine r epeat, and C-terminal domains (2010)
  • Author(s): T. Ogura, K.I. Tong, K. Mio, Y. Maruyam a, H. Kurokawa, C. Sato, M. Yamamoto.
  • Journal Title: Proc. Natl. Acad. Sci. U S A 107 Pages: 2842-2847
  • Peer Reviewed
• [Journal Article] Atmospheric scanning elect ron microscope observes cells and t issues in open medium through silic on nitride film (2010)
  • Author(s): H. Nishiyama, M. Suga, T. Ogura, Y. Mar uyama, M. Koizumi, K. Mio, S. Kitamura, C. Sato.
  • Journal Title: J Struct. Biol. 169 Pages: 438-449
  • Peer Reviewed
• [Journal Article] Tetrameric orai1 is a teard rop-shaped molecule with a long, ta pered cytoplasmic domain (2009)
  • Author(s): Y. Maruyama, T. Ogura, K. Mio, K. Kato, T. Kaneko, S. Kiyonaka, Y. Mori, C. Sato
  • Journal Title: J. Biol. Chem. 284(20) Pages: 13676-13685
  • Peer Reviewed
• [Journal Article] Selective and direct i nhibition of TRPC3 channels underli es biological activities of a pyraz ole compound (2009)
  • Author(s): S. Kiyonaka, K. Kato, M. Nishida, K. Mi o, T. Numaga, Y. Sawaguchi, T. Yoshida, M. Wakamori, E. Mori, T. Numata, M. Is hii, H. Takemoto, A. Ojida, K. Watanab e, A. Uemura, H. Kurose, T. Morii, T. K obayashi, Y. Sato, C. Sato, I. Hamachi, Y. Mori
  • Journal Title: PNAS 106(13) Pages: 5400-5405
  • Peer Reviewed
• [Journal Article] Three-dimensional reconstruction of Human CFTR chloride channel revea led an ellipsoidal structure with o rifices beneath the putative tran smembrane domain (2008)
  • Author(s): K. Mio, T. Ogura, M. Mio, H. Shimizu, TC. Hwang, C. Sato, Y. Sohma
  • Journal Title: J. Biol. Chem. 283(44) Pages: 30300-30310
  • Peer Reviewed
• [Journal Article] The motor prote in prestin is a bullet-shaped molec ule with inner cavities (2008)
  • Author(s): K. Mio, Y. Kubo, T. Ogura, T. Yamamoto, F. Arisaka, C. Sato
  • Journal Title: J. Biol. Chem. 283(2) Pages: 1137-1145
  • Peer Reviewed
• [Journal Article] Threedimensional reconstruction using tr ansmission EM reveals a swollen, be ll-shaped structure of TRPM2 cation channel (2007)
  • Author(s): Y. Maruyama, T. Ogura, K. Mio, S. Kiyon aka, K. Kato, Y. Mori, C. Sato
  • Journal Title: J. Biol. Chem. 282(51) Pages: 36961-36970
  • Peer Reviewed
• [Journal Article] TRIC channels are essential for Ca2+ handling in intracellular stores (2007)
  • Author(s): M. Yazawa, C. Ferrante, J. Feng, K. Mio, T. Ogura, M. Zhang, P-H. Lin, Z. Pan, S. Komazaki, K. Kato, M. Nishi, X. Zhao, N. Weisleder, C. Sato, J. Ma, H. Tak eshima
  • Journal Title: Nature 448(7149) Pages: 78-82
  • Peer Reviewed
• [Journal Article] A fully automat ic 3D reconstruction method using s imulated annealing enables accurat e posterioric angular assignment of protein projections (2006)
  • Author(s): T. Ogura, C. Sato
  • Journal Title: J. Struct. Biol. 156 Pages: 371-386
  • Peer Reviewed
• [Presentation] The Atmospheric Sem Observ es Nuclei in the Surface Level of T issue Without Thin-Sectioning (2009)
  • Author(s): C. Sato
  • Organizer: The American Society for Cell Biology 4 9th Annual Meeting
  • Place of Presentation: サンディエゴ
  • Year and Date: 2009-12-08
• [Presentation] Three-dimensional structu res of ion channels revealed by ele ctron microscopy: sodium, TRP, CFTR and Orai1 channels (2009)
  • Author(s): C. Sato
  • Organizer: Neuroscience 2 009
  • Place of Presentation: シカゴ
  • Year and Date: 2009-10-21
• [Presentation] Maximum likelihood appr oach for picking-up process in sing le particle analysis (2008)
  • Author(s): M. Kawata
  • Organizer: 第46回日本生物物理学会年会
  • Place of Presentation: 福岡市
  • Year and Date: 2008-12-05
• [Presentation] 単粒子解析によるTRP channe l family間での構造比較. Structure of TRP channels revealed by single particle analysis using EM images (2008)
  • Author(s): M. Kawata
  • Organizer: 第46回日本生物物理学会年会
  • Place of Presentation: 福岡市
  • Year and Date: 2008-12-03
• [Presentation] The 3D structure of ion c hannels, sensors and receptors reve aled by electron microscopy (2008)
  • Author(s): T. Ogura
  • Organizer: Inter national Conference of Physiologica l Sciences and 11th International S ymposium on Molecular Medicine, Cr ete
  • Place of Presentation: Greece
  • Year and Date: 2008-10-09
• [Remarks]
  • URL: http://unit.aist.go.jp/neurosci/japanese/group/kouzouseiri.html
• [Patent(Industrial Property Rights)] 構造推定システム、構造推定方法およびプログラム (2010)
  • Inventor(s): 川田正晃、佐藤主税
  • Industrial Property Rights Holder: 独立行政法人産業技術総合研究所
  • Industrial Property Number: 特許US-2010-0067809-A1
  • Filing Date: 2010-03-18
• [Patent(Industrial Property Rights)] 画像処理システム、画像処理方法、プログラムおよび記録媒体 (2008)
  • Inventor(s): 川田正晃、佐藤主税
  • Industrial Property Rights Holder: 独立行政法人産業技術総合研究所
  • Industrial Property Number: 特許特願2008-289005
  • Filing Date: 2008-11-11
• [Patent(Industrial Property Rights)] 構造推定システム、構造推定方法およびプログラム (2008)
  • Inventor(s): 川田正晃、佐藤主税
  • Industrial Property Rights Holder: 独立行政法人産業技術総合研究所
  • Industrial Property Number: 特許4171919
  • Filing Date: 2008-08-22
• [Patent(Industrial Property Rights)] 電子顕微鏡観察像の画像処理方法および画像処理プログラム並びに記録媒体 (2007)
  • Inventor(s): 小椋俊彦、佐藤主税、藤吉好則
  • Industrial Property Rights Holder: 独立行政法人産業技術総合研究所
  • Industrial Property Number: 特許3968421
  • Acquisition Date: 2007-06-15