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Literature DB >> 24813624

Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL.

Kunio Hirata¹, Kyoko Shinzawa-Itoh², Naomine Yano³, Shuhei Takemura⁴, Koji Kato², Miki Hatanaka⁴, Kazumasa Muramoto⁴, Takako Kawahara⁴, Tomitake Tsukihara⁵, Eiki Yamashita⁶, Kensuke Tono⁷, Go Ueno⁸, Takaaki Hikima⁸, Hironori Murakami⁸, Yuichi Inubushi⁸, Makina Yabashi⁸, Tetsuya Ishikawa⁸, Masaki Yamamoto⁸, Takashi Ogura⁹, Hiroshi Sugimoto⁸, Jian-Ren Shen¹⁰, Shinya Yoshikawa⁴, Hideo Ago⁸.

Abstract

We report a method of femtosecond crystallography for solving radiation damage-free crystal structures of large proteins at sub-angstrom spatial resolution, using a large single crystal and the femtosecond pulses of an X-ray free-electron laser (XFEL). We demonstrated the performance of the method by determining a 1.9-Å radiation damage-free structure of bovine cytochrome c oxidase, a large (420-kDa), highly radiation-sensitive membrane protein.

Entities: Gene Species

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Year: 2014 PMID： 24813624 DOI： 10.1038/nmeth.2962

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

26 in total

1. Potential for biomolecular imaging with femtosecond X-ray pulses.

Authors: R Neutze; R Wouts; D van der Spoel; E Weckert; J Hajdu
Journal: Nature Date: 2000-08-17 Impact factor: 49.962

2. Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å.

Authors: Yasufumi Umena; Keisuke Kawakami; Jian-Ren Shen; Nobuo Kamiya
Journal: Nature Date: 2011-04-17 Impact factor: 49.962

3. Resolution of phase ambiguity in macromolecular crystallography.

Authors: B C Wang
Journal: Methods Enzymol Date: 1985 Impact factor: 1.600

4. Structural basis of biological N2O generation by bacterial nitric oxide reductase.

Authors: Tomoya Hino; Yushi Matsumoto; Shingo Nagano; Hiroshi Sugimoto; Yoshihiro Fukumori; Takeshi Murata; So Iwata; Yoshitsugu Shiro
Journal: Science Date: 2010-11-25 Impact factor: 47.728

Review 5. Proton-pumping mechanism of cytochrome C oxidase.

Authors: Shinya Yoshikawa; Kazumasa Muramoto; Kyoko Shinzawa-Itoh
Journal: Annu Rev Biophys Date: 2011 Impact factor: 12.981

6. Structures of metal sites of oxidized bovine heart cytochrome c oxidase at 2.8 A.

Authors: T Tsukihara; H Aoyama; E Yamashita; T Tomizaki; H Yamaguchi; K Shinzawa-Itoh; R Nakashima; R Yaono; S Yoshikawa
Journal: Science Date: 1995-08-25 Impact factor: 47.728

7. A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump.

Authors: Hiroshi Aoyama; Kazumasa Muramoto; Kyoko Shinzawa-Itoh; Kunio Hirata; Eiki Yamashita; Tomitake Tsukihara; Takashi Ogura; Shinya Yoshikawa
Journal: Proc Natl Acad Sci U S A Date: 2009-01-21 Impact factor: 11.205

Review 8. Scaling and assessment of data quality.

Authors: Philip Evans
Journal: Acta Crystallogr D Biol Crystallogr Date: 2005-12-14

9. How good are my data and what is the resolution?

Authors: Philip R Evans; Garib N Murshudov
Journal: Acta Crystallogr D Biol Crystallogr Date: 2013-06-13

10. An introduction to data reduction: space-group determination, scaling and intensity statistics.

Authors: Philip R Evans
Journal: Acta Crystallogr D Biol Crystallogr Date: 2011-03-18

92 in total

1. Cardiolipin Interactions with Proteins.

Authors: Joan Planas-Iglesias; Himal Dwarakanath; Dariush Mohammadyani; Naveena Yanamala; Valerian E Kagan; Judith Klein-Seetharaman
Journal: Biophys J Date: 2015-08-20 Impact factor: 4.033

2. Observation of femtosecond X-ray interactions with matter using an X-ray-X-ray pump-probe scheme.

Authors: Ichiro Inoue; Yuichi Inubushi; Takahiro Sato; Kensuke Tono; Tetsuo Katayama; Takashi Kameshima; Kanade Ogawa; Tadashi Togashi; Shigeki Owada; Yoshiyuki Amemiya; Takashi Tanaka; Toru Hara; Makina Yabashi
Journal: Proc Natl Acad Sci U S A Date: 2016-01-25 Impact factor: 11.205

3. Oxygen additions in serial femtosecond crystallographic protein structures.

Authors: Jimin Wang
Journal: Protein Sci Date: 2016-07-26 Impact factor: 6.725

4. Snapshot of an oxygen intermediate in the catalytic reaction of cytochrome c oxidase.

Authors: Izumi Ishigami; Ariel Lewis-Ballester; Austin Echelmeier; Gerrit Brehm; Nadia A Zatsepin; Thomas D Grant; Jesse D Coe; Stella Lisova; Garrett Nelson; Shangji Zhang; Zachary F Dobson; Sébastien Boutet; Raymond G Sierra; Alexander Batyuk; Petra Fromme; Raimund Fromme; John C H Spence; Alexandra Ros; Syun-Ru Yeh; Denis L Rousseau
Journal: Proc Natl Acad Sci U S A Date: 2019-02-11 Impact factor: 11.205

5. X-ray structures of catalytic intermediates of cytochrome c oxidase provide insights into its O₂ activation and unidirectional proton-pump mechanisms.

Authors: Atsuhiro Shimada; Yuki Etoh; Rika Kitoh-Fujisawa; Ai Sasaki; Kyoko Shinzawa-Itoh; Takeshi Hiromoto; Eiki Yamashita; Kazumasa Muramoto; Tomitake Tsukihara; Shinya Yoshikawa
Journal: J Biol Chem Date: 2020-03-12 Impact factor: 5.157

Review 6. A Bright Future for Serial Femtosecond Crystallography with XFELs.

Authors: Linda C Johansson; Benjamin Stauch; Andrii Ishchenko; Vadim Cherezov
Journal: Trends Biochem Sci Date: 2017-07-18 Impact factor: 13.807

Review 7. Proton translocation in cytochrome c oxidase: insights from proton exchange kinetics and vibrational spectroscopy.

Authors: Izumi Ishigami; Masahide Hikita; Tsuyoshi Egawa; Syun-Ru Yeh; Denis L Rousseau
Journal: Biochim Biophys Acta Date: 2014-09-28