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

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

doi:10.1038/srep35279

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 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. As a result, the study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.

Authors:

Edlund, Petra ^[1]; Takala, Heikki ^[2]; Claesson, Elin ^[1]; Henry, Léocadie ^[1]; Dods, Robert ^[1]; Lehtivuori, Heli ^[3]; Panman, Matthijs ^[1]; Pande, Kanupriya ^[4]; White, Thomas ^[4]; Nakane, Takanori ^[5]; Berntsson, Oskar ^[1]; Gustavsson, Emil ^[1]; Båth, Petra ^[1]; Modi, Vaibhav ^[3]; Roy-Chowdhury, Shatabdi ^[6]; Zook, James ^[6]; Berntsen, Peter ^[7]; Pandey, Suraj ^[8]; Poudyal, Ishwor ^[8]; Tenboer, Jason ^[8] more »

Univ. of Gothenburg, Gothenburg (Sweden)
Univ. of Gothenburg, Gothenburg (Sweden); Univ. of Jyvaskyla, Jyvaskyla (Finland); Univ. of Helsinki, Helsinki (Finland)
Univ. of Jyvaskyla, Jyvaskyla (Finland)
Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)
The Univ. of Tokyo, Tokyo (Japan)
Arizona State Univ., Tempe, AZ (United States)
LaTrobe Univ., Melbourne, VIC (Australia)
Univ. of Wisconsin, Milwaukee, WI (United States)
SLAC National Accelerator Lab., Menlo Park, CA (United States)
RIKEN SPring-8 Center, Hyogo (Japan)
Univ. of Chicago, Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
Northern Illinois Univ., Chicago, IL (United States)

Publication Date:: Wed Oct 19 00:00:00 EDT 2016

Research Org.:: SLAC National Accelerator Lab., Menlo Park, CA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1348400

Grant/Contract Number:: AC02-76SF00515

Resource Type:: Accepted Manuscript

Journal Name:: Scientific Reports

Additional Journal Information:: Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2045-2322

Publisher:: Nature Publishing Group

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; chemical biology; proteins

Citation Formats


                    Edlund, Petra, Takala, Heikki, Claesson, Elin, Henry, Léocadie, Dods, Robert, Lehtivuori, Heli, Panman, Matthijs, Pande, Kanupriya, White, Thomas, Nakane, Takanori, Berntsson, Oskar, Gustavsson, Emil, Båth, Petra, Modi, Vaibhav, Roy-Chowdhury, Shatabdi, Zook, James, Berntsen, Peter, Pandey, Suraj, Poudyal, Ishwor, Tenboer, Jason, Kupitz, Christopher, Barty, Anton, Fromme, Petra, Koralek, Jake D., Tanaka, Tomoyuki, Spence, John, Liang, Mengning, Hunter, Mark S., Boutet, Sebastien, Nango, Eriko, Moffat, Keith, Groenhof, Gerrit, Ihalainen, Janne, Stojković, Emina A., Schmidt, Marius, and Westenhoff, Sebastian. The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography.  United States: N. p., 2016. 
Web.  doi:10.1038/srep35279.

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                    Edlund, Petra, Takala, Heikki, Claesson, Elin, Henry, Léocadie, Dods, Robert, Lehtivuori, Heli, Panman, Matthijs, Pande, Kanupriya, White, Thomas, Nakane, Takanori, Berntsson, Oskar, Gustavsson, Emil, Båth, Petra, Modi, Vaibhav, Roy-Chowdhury, Shatabdi, Zook, James, Berntsen, Peter, Pandey, Suraj, Poudyal, Ishwor, Tenboer, Jason, Kupitz, Christopher, Barty, Anton, Fromme, Petra, Koralek, Jake D., Tanaka, Tomoyuki, Spence, John, Liang, Mengning, Hunter, Mark S., Boutet, Sebastien, Nango, Eriko, Moffat, Keith, Groenhof, Gerrit, Ihalainen, Janne, Stojković, Emina A., Schmidt, Marius, & Westenhoff, Sebastian. The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography.  United States.  https://doi.org/10.1038/srep35279

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                    Edlund, Petra, Takala, Heikki, Claesson, Elin, Henry, Léocadie, Dods, Robert, Lehtivuori, Heli, Panman, Matthijs, Pande, Kanupriya, White, Thomas, Nakane, Takanori, Berntsson, Oskar, Gustavsson, Emil, Båth, Petra, Modi, Vaibhav, Roy-Chowdhury, Shatabdi, Zook, James, Berntsen, Peter, Pandey, Suraj, Poudyal, Ishwor, Tenboer, Jason, Kupitz, Christopher, Barty, Anton, Fromme, Petra, Koralek, Jake D., Tanaka, Tomoyuki, Spence, John, Liang, Mengning, Hunter, Mark S., Boutet, Sebastien, Nango, Eriko, Moffat, Keith, Groenhof, Gerrit, Ihalainen, Janne, Stojković, Emina A., Schmidt, Marius, and Westenhoff, Sebastian. Wed .  
"The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography".  United States.  https://doi.org/10.1038/srep35279.  https://www.osti.gov/servlets/purl/1348400.

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@article{osti_1348400,

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

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

  abstractNote = {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. As a result, the study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.},

  doi          = {10.1038/srep35279},

  journal      = {Scientific Reports},

  number       = 1,

  volume       = 6,

  place        = {United States},

  year         = {Wed Oct 19 00:00:00 EDT 2016},

  month        = {Wed Oct 19 00:00:00 EDT 2016}

}

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