The structure analysis of PBCV-1 by the combination of X-ray crystallography and coherent X-ray diffraction imaging

• Project/Area Number: 15K06971
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Osaka University
• Principal Investigator: Higashiura Akifumi 大阪大学, たんぱく質研究所, 助教 (90598129)
• Project Period (FY): 2015-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2017: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2016: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2015: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
• Keywords: Ｘ線結晶解析 / コヒーレントＸ線イメージング / 構造生物学

Outline of Final Research Achievements

Studies aimed at the structure analysis of a giant virus, PBCV-1 by the combination of X-ray crystallography and coherent X-ray diffraction imaging was carried out. The single crystals of PBCV1 have not been obtained yet, but the technical improvements were proceeded using the other virus crystals as a model. The high-resolution diffraction patterns were successfully observed from viral fragile crystals.
In the experiment of coherent X-ray diffraction imaging, so many diffraction patterns from PBCV-1 were collected and processed for 2D imaging. The data selection of diffraction data from huge data set is carrying out aimed to the 3D reconstruction of PBCV-1.

Research Products

• [Int'l Joint Research] ウプサラ大学(スウェーデン)
• [Int'l Joint Research] ウプサラ大学(スウェーデン)
• [Int'l Joint Research] Uppsala university(Sweden)
• [Journal Article] Hierarchical structure assembly model of rice dwarf virus particle formation. (2018)
  • Author(s): Nakagawa A., Miyazaki N., Higashiura A.
  • Journal Title: Biophys Rev. Volume: 10(2) Issue: 2 Pages: 659-665
  • DOI: 10.1007/s12551-017-0375-2
  • Peer Reviewed / Open Access
• [Journal Article] Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source (2016)
  • Author(s): Munke A.,…,Daurer B.J.,…,Hajdu J.,Hantke M.F.,Higashiura A.,…,Kumar H.,…,Maia F.R.N.C.,…,Nakagawa A.,…,Okamoto K., …,van der Schot G.,…,Seibert M.M.,…,Svenda M.,et al
  • Journal Title: Scientific Data Volume: 3 Issue: 1 Pages: 160064-160064
  • DOI: 10.1038/sdata.2016.64
  • Peer Reviewed / Open Access
• [Presentation] Structure assembly mechanism of Rice Dwarf Virus (2017)
  • Author(s): Higashiura, A.; Nakamichi, Y.; Miyazaki, N.; Tsutsumi, K.; Iwasaki, K.; Murata, K.; Omura, T. & Nakagawa, A.
  • Organizer: IUCr
  • Int'l Joint Research
• [Presentation] SPring-8 BL44XU, A Beamline Designed for Structure Analysis of Large Biological Macromolecular Assemblies (2016)
  • Author(s): Yamashita E., Higashiura A., Yoshimura M., Hasegawa K., Furukawa Y., Kumasaka T., Ueno G., Yamamoto M., Tsukihara T., Nakagawa A.
  • Organizer: 5th International symposium on diffraction structural biology
  • Place of Presentation: Knoxville, US
  • Year and Date: 2016-08-07
  • Int'l Joint Research
• [Presentation] Approaches for Coherent X-ray Diffraction Imaging of Paramecium bursaria Chlorella virus-1 (2015)
  • Author(s): Akifumi Higashiura, Gijs van der Schot, Max Hantke, Jing Liu, Takashi Yamada, Janos Hajdu, Atsushi Nakagawa
  • Organizer: The 13th Conference of the Asian Crystallographic Association
  • Place of Presentation: Kolkata, India
  • Year and Date: 2015-12-05
  • Int'l Joint Research
• [Presentation] 高圧凍結法を用いたイネ萎縮ウイルスの高分解能Ｘ線結晶構造解析への取り組み (2015)
  • Author(s): 東浦 彰史, 中道 優介, 太田 和敬, 宮崎 直幸, 一木 珠樹, 大村 敏博, 中川 敦史
  • Organizer: 平成２７年度 日本結晶学会 年会
  • Place of Presentation: 大阪府立大学中百舌鳥キャンパス（大阪）
  • Year and Date: 2015-10-17
• [Presentation] SPring-8 BL44XU, Beamline Designed for Structure Analysis of Large Biological Macromolecular Assemblies (2015)
  • Author(s): Akifumi Higashiura, Eiki Yamashita, Masato Yoshimura, Kazuya Hasegawa, Yukito Furukawa, Takashi Kumasaka, Go Ueno, Masaki Yamamoto, Tomitake Tsukihara, Atsushi Nakagawa
  • Organizer: 12th International Conference on Synchrotron Radiation Instrumentation
  • Place of Presentation: New York, USA
  • Year and Date: 2015-07-06
  • Int'l Joint Research