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Review
. 2018 Apr;10(2):209-218.
doi: 10.1007/s12551-017-0344-9. Epub 2017 Dec 1.

Serial femtosecond crystallography at the SACLA: breakthrough to dynamic structural biology

Eiichi Mizohata  1   2 , Takanori Nakane  3   4 , Yohta Fukuda  5 , Eriko Nango  6   7 , So Iwata  6   7
Affiliations
Review

Serial femtosecond crystallography at the SACLA: breakthrough to dynamic structural biology

Eiichi Mizohata et al. Biophys Rev. 2018 Apr.

Abstract

X-ray crystallography visualizes the world at the atomic level. It has been used as the most powerful technique for observing the three-dimensional structures of biological macromolecules and has pioneered structural biology. To determine a crystal structure with high resolution, it was traditionally required to prepare large crystals (> 200 μm). Later, synchrotron radiation facilities, such as SPring-8, that produce powerful X-rays were built. They enabled users to obtain good quality X-ray diffraction images even with smaller crystals (ca. 200-50 μm). In recent years, one of the most important technological innovations in structural biology has been the development of X-ray free electron lasers (XFELs). The SPring-8 Angstrom Compact free electron LAser (SACLA) in Japan generates the XFEL beam by accelerating electrons to relativistic speeds and directing them through in-vacuum, short-period undulators. Since user operation started in 2012, we have been involved in the development of serial femtosecond crystallography (SFX) measurement systems using XFEL at the SACLA. The SACLA generates X-rays a billion times brighter than SPring-8. The extremely bright XFEL pulses enable data collection with microcrystals (ca. 50-1 μm). Although many molecular analysis techniques exist, SFX is the only technique that can visualize radiation-damage-free structures of biological macromolecules at room temperature in atomic resolution and fast time resolution. Here, we review the achievements of the SACLA-SFX Project in the past 5 years. In particular, we focus on: (1) the measurement system for SFX; (2) experimental phasing by SFX; (3) enzyme chemistry based on damage-free room-temperature structures; and (4) molecular movie taken by time-resolved SFX.

Keywords: Bioinorganic chemistry; De novo phasing; Detergent; Membrane protein; Structure–function relationship; Time-resolved analysis.

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Conflict of interest statement

Conflict of interest

Eiichi Mizohata declares that he has no conflict of interest. Takanori Nakane declares that he has no conflict of interest. Yohta Fukuda declares that he has no conflict of interest. Eriko Nango declares that she has no conflict of interest. So Iwata declares that he has no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Figures

Fig. 1
Fig. 1
The X-ray free electron laser (XFEL), a new technological innovation in structural biology. a The XFEL facility, the SPring-8 Angstrom Compact free electron LAser (SACLA), is built next to SPring-8 in Harima Science Garden City, Hyogo, Japan. b The serial femtosecond crystallography (SFX) measurement scheme at the SACLA. A pump laser can be used for data collection in time-resolved SFX
Fig. 2
Fig. 2
SFX and synchrotron radiation crystallography (SRX) structures of Alcaligenes faecalis copper-containing nitrite reductase (CuNiR) (AfNiR). a The T2Cu site of the SFX resting state (RS) structure (PDB ID: 4YSC). b Structural difference of His255 between the SRX RS structure (yellow, PDB ID: 4YSE) and the SFX RS structure (green, PDB ID: 4YSC). Water molecules and Cu atoms are shown as spheres. The dashed yellow lines show hydrogen bonds. c Superposition of the SFX nitrite complex (NC) structure (red, PDB ID: 5D4I) on the SRX NC structure (blue, PDB ID: 5D4H)
Fig. 3
Fig. 3
Four snapshots from a molecular movie of bacteriorhodopsin (bR) taken by time-resolved SFX. Structures of bR at four selected delay time points—16 ns, 760 ns, 36.2 μs, and 1725 μs—are drawn as ribbon models. Blue and yellow meshes represent positive and negative |F obs|light–|F obs|dark difference Fourier electron density maps, respectively
See this image and copyright information in PMC

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