The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

Petra Edlund; Heikki Takala; Elin Claesson; Leócadie Henry; Robert Dods; Heli Lehtivuori; Matthijs Panman; Kanupriya Pande; Thomas White; Takanori Nakane; Oskar Berntsson; Emil Gustavsson; Petra Båth; Vaibhav Modi; Shatabdi Roy-Chowdhury; James Zook; Peter Berntsen; Suraj Pandey; Ishwor Poudyal; Jason Tenboer; Christopher Kupitz; Anton Barty; Petra Fromme; Jake D. Koralek; Tomoyuki Tanaka; John Spence; Mengning Liang; Mark S. Hunter; Sebastien Boutet; Eriko Nango; Keith Moffat; Gerrit Groenhof; Janne Ihalainen; Emina A. Stojkovi; Marius Schmidt; Sebastian Westenhoff

doi:10.1038/srep35279

The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

Petra Edlund, Heikki Takala, Elin Claesson, Leócadie Henry, Robert Dods, Heli Lehtivuori, Matthijs Panman, Kanupriya Pande, Thomas White, Takanori Nakane, Oskar Berntsson, Emil Gustavsson, Petra Båth, Vaibhav Modi, Shatabdi Roy-Chowdhury, James Zook, Peter Berntsen, Suraj Pandey, Ishwor Poudyal, Jason TenboerChristopher Kupitz, Anton Barty, Petra Fromme, Jake D. Koralek, Tomoyuki Tanaka, John Spence, Mengning Liang, Mark S. Hunter, Sebastien Boutet, Eriko Nango, Keith Moffat, Gerrit Groenhof, Janne Ihalainen, Emina A. Stojkovi, Marius Schmidt, Sebastian Westenhoff

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Abstract

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.

Original language	English (US)
Article number	35279
Journal	Scientific reports
Volume	6
DOIs	https://doi.org/10.1038/srep35279
State	Published - Oct 19 2016

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Edlund, P., Takala, H., Claesson, E., Henry, L., Dods, R., Lehtivuori, H., Panman, M., Pande, K., White, T., Nakane, T., Berntsson, O., Gustavsson, E., Båth, P., Modi, V., Roy-Chowdhury, S., Zook, J., Berntsen, P., Pandey, S., Poudyal, I., ... Westenhoff, S. (2016). The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography. Scientific reports, 6, Article 35279. https://doi.org/10.1038/srep35279

Edlund, P, Takala, H, Claesson, E, Henry, L, Dods, R, Lehtivuori, H, Panman, M, Pande, K, White, T, Nakane, T, Berntsson, O, Gustavsson, E, Båth, P, Modi, V, Roy-Chowdhury, S, Zook, J, Berntsen, P, Pandey, S, Poudyal, I, Tenboer, J, Kupitz, C, Barty, A, Fromme, P, Koralek, JD, Tanaka, T, Spence, J, Liang, M, Hunter, MS, Boutet, S, Nango, E, Moffat, K, Groenhof, G, Ihalainen, J, Stojkovi, EA, Schmidt, M & Westenhoff, S 2016, 'The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography', Scientific reports, vol. 6, 35279. https://doi.org/10.1038/srep35279

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title = "The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography",

abstract = "Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 {\AA} resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 {\AA} resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.",

author = "Petra Edlund and Heikki Takala and Elin Claesson and Le{\'o}cadie Henry and Robert Dods and Heli Lehtivuori and Matthijs Panman and Kanupriya Pande and Thomas White and Takanori Nakane and Oskar Berntsson and Emil Gustavsson and Petra B{\aa}th and Vaibhav Modi and Shatabdi Roy-Chowdhury and James Zook and Peter Berntsen and Suraj Pandey and Ishwor Poudyal and Jason Tenboer and Christopher Kupitz and Anton Barty and Petra Fromme and Koralek, {Jake D.} and Tomoyuki Tanaka and John Spence and Mengning Liang and Hunter, {Mark S.} and Sebastien Boutet and Eriko Nango and Keith Moffat and Gerrit Groenhof and Janne Ihalainen and Stojkovi, {Emina A.} and Marius Schmidt and Sebastian Westenhoff",

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doi = "10.1038/srep35279",

language = "English (US)",

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AU - Edlund, Petra

AU - Takala, Heikki

AU - Claesson, Elin

AU - Henry, Leócadie

AU - Dods, Robert

AU - Lehtivuori, Heli

AU - Panman, Matthijs

AU - Pande, Kanupriya

AU - White, Thomas

AU - Nakane, Takanori

AU - Berntsson, Oskar

AU - Gustavsson, Emil

AU - Båth, Petra

AU - Modi, Vaibhav

AU - Roy-Chowdhury, Shatabdi

AU - Zook, James

AU - Berntsen, Peter

AU - Pandey, Suraj

AU - Poudyal, Ishwor

AU - Tenboer, Jason

AU - Kupitz, Christopher

AU - Barty, Anton

AU - Fromme, Petra

AU - Koralek, Jake D.

AU - Tanaka, Tomoyuki

AU - Spence, John

AU - Liang, Mengning

AU - Hunter, Mark S.

AU - Boutet, Sebastien

AU - Nango, Eriko

AU - Moffat, Keith

AU - Groenhof, Gerrit

AU - Ihalainen, Janne

AU - Stojkovi, Emina A.

AU - Schmidt, Marius

AU - Westenhoff, Sebastian

PY - 2016/10/19

Y1 - 2016/10/19

N2 - Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.

AB - Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.

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The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

Abstract

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Wild-type PAS-GAF fragment from Deinococcus radiodurans BphP

Wild-type PAS-GAF fragment from Deinococcus radiodurans Bphp collected at SACLA

Wild-type PAS-GAF fragment from Deinococcus radiodurans Bphp collected at LCLS

Cite this

The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Datasets

Wild-type PAS-GAF fragment from Deinococcus radiodurans BphP

Wild-type PAS-GAF fragment from Deinococcus radiodurans Bphp collected at SACLA

Wild-type PAS-GAF fragment from Deinococcus radiodurans Bphp collected at LCLS

Cite this