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Comment
. 2016 Aug 1:3:160057.
doi: 10.1038/sdata.2016.57.

Serial femtosecond crystallography datasets from G protein-coupled receptors

Thomas A White  1 , Anton Barty  1 , Wei Liu  2 , Andrii Ishchenko  3 , Haitao Zhang  3 , Cornelius Gati  4 , Nadia A Zatsepin  5 , Shibom Basu  2 , Dominik Oberthür  1 , Markus Metz  1 , Kenneth R Beyerlein  1 , Chun Hong Yoon  1 , Oleksandr M Yefanov  1 , Daniel James  6 , Dingjie Wang  7 , Marc Messerschmidt  8 , Jason E Koglin  9 , Sébastien Boutet  9 , Uwe Weierstall  5 , Vadim Cherezov  3
Affiliations
Comment

Serial femtosecond crystallography datasets from G protein-coupled receptors

Thomas A White et al. Sci Data. .

Abstract

We describe the deposition of four datasets consisting of X-ray diffraction images acquired using serial femtosecond crystallography experiments on microcrystals of human G protein-coupled receptors, grown and delivered in lipidic cubic phase, at the Linac Coherent Light Source. The receptors are: the human serotonin receptor 2B in complex with an agonist ergotamine, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH2, the human smoothened receptor in complex with an antagonist cyclopamine, and finally the human angiotensin II type 1 receptor in complex with the selective antagonist ZD7155. All four datasets have been deposited, with minimal processing, in an HDF5-based file format, which can be used directly for crystallographic processing with CrystFEL or other software. We have provided processing scripts and supporting files for recent versions of CrystFEL, which can be used to validate the data.

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Conflict of interest statement

U.W. has filed a patent application (US 20160051995) for the LCP injector. The remaining authors declare no competing financial interests.

Figures

Figure 1
Figure 1. Schematic diagram of an LCP-SFX experiment.
The stream of crystal-containing LCP is extruded from the LCP injector into the focus of the X-ray beam, formed by upstream optics (Kirkpatrick-Baez mirrors in this case). The LCP stream is kept straight by a coaxially flowing gas stream, indicated by the curved blue dashed lines. The X-ray beam is represented by the orange cylinder. Diffracted X-rays are measured by the detector (far left). The unscattered X-ray beam passes through a hole in the center of the detector. The LCP injector and CSPAD detector are located inside a sample vacuum chamber (dotted line). Adapted from (ref. 3).
Figure 2
Figure 2. Representative diffraction patterns from (a) 5-HT2B, (b) AT1R, (c) SMO and (d) δ-OR.
The solid grey areas are the regions outside the panels of the detector. The diffuse circle arises from the LCP matrix, and sharp spots from the crystals. Pattern (d) is shown with calculated reflection positions circled, but (a–c) are not.
Figure 3
Figure 3. Plots of the self-consistency figures of merit (a) Rsplit and (b) CC1/2 against resolution for all four datasets as re-processed here.
Figure 4
Figure 4. Plots of the signal-to-noise ratio I/sigma(I) for all four datasets as reprocessed here.
See this image and copyright information in PMC

Comment on

  • Serial femtosecond crystallography of G protein-coupled receptors.
    Liu W, Wacker D, Gati C, Han GW, James D, Wang D, Nelson G, Weierstall U, Katritch V, Barty A, Zatsepin NA, Li D, Messerschmidt M, Boutet S, Williams GJ, Koglin JE, Seibert MM, Wang C, Shah ST, Basu S, Fromme R, Kupitz C, Rendek KN, Grotjohann I, Fromme P, Kirian RA, Beyerlein KR, White TA, Chapman HN, Caffrey M, Spence JC, Stevens RC, Cherezov V. Liu W, et al. Science. 2013 Dec 20;342(6165):1521-4. doi: 10.1126/science.1244142. Science. 2013. PMID: 24357322 Free PMC article.
  • Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography.
    Weierstall U, James D, Wang C, White TA, Wang D, Liu W, Spence JC, Bruce Doak R, Nelson G, Fromme P, Fromme R, Grotjohann I, Kupitz C, Zatsepin NA, Liu H, Basu S, Wacker D, Han GW, Katritch V, Boutet S, Messerschmidt M, Williams GJ, Koglin JE, Marvin Seibert M, Klinker M, Gati C, Shoeman RL, Barty A, Chapman HN, Kirian RA, Beyerlein KR, Stevens RC, Li D, Shah ST, Howe N, Caffrey M, Cherezov V. Weierstall U, et al. Nat Commun. 2014;5:3309. doi: 10.1038/ncomms4309. Nat Commun. 2014. PMID: 24525480 Free PMC article.
  • Structural basis for bifunctional peptide recognition at human δ-opioid receptor.
    Fenalti G, Zatsepin NA, Betti C, Giguere P, Han GW, Ishchenko A, Liu W, Guillemyn K, Zhang H, James D, Wang D, Weierstall U, Spence JC, Boutet S, Messerschmidt M, Williams GJ, Gati C, Yefanov OM, White TA, Oberthuer D, Metz M, Yoon CH, Barty A, Chapman HN, Basu S, Coe J, Conrad CE, Fromme R, Fromme P, Tourwé D, Schiller PW, Roth BL, Ballet S, Katritch V, Stevens RC, Cherezov V. Fenalti G, et al. Nat Struct Mol Biol. 2015 Mar;22(3):265-8. doi: 10.1038/nsmb.2965. Epub 2015 Feb 16. Nat Struct Mol Biol. 2015. PMID: 25686086 Free PMC article.
  • Structure of the Angiotensin receptor revealed by serial femtosecond crystallography.
    Zhang H, Unal H, Gati C, Han GW, Liu W, Zatsepin NA, James D, Wang D, Nelson G, Weierstall U, Sawaya MR, Xu Q, Messerschmidt M, Williams GJ, Boutet S, Yefanov OM, White TA, Wang C, Ishchenko A, Tirupula KC, Desnoyer R, Coe J, Conrad CE, Fromme P, Stevens RC, Katritch V, Karnik SS, Cherezov V. Zhang H, et al. Cell. 2015 May 7;161(4):833-44. doi: 10.1016/j.cell.2015.04.011. Epub 2015 Apr 23. Cell. 2015. PMID: 25913193 Free PMC article.
  • The trickle before the torrent-diffraction data from X-ray lasers.
    Maia FR, Hajdu J. Maia FR, et al. Sci Data. 2016 Aug 1;3:160059. doi: 10.1038/sdata.2016.59. Sci Data. 2016. PMID: 27479637 Free PMC article.

References

Data Citations

    1. Liu W. 2013. Coherent X-ray Imaging Data Bank. http://dx.doi.org/10.11577/1169541 - DOI
    1. Weierstall U. 2016. Coherent X-ray Imaging Data Bank. http://dx.doi.org/10.11577/1255979 - DOI
    1. Fenalti G. 2016. Coherent X-ray Imaging Data Bank. http://dx.doi.org/10.11577/1255980 - DOI
    1. Zhang H. 2016. Coherent X-ray Imaging Data Bank. http://dx.doi.org/10.11577/1255978 - DOI

References

    1. Chapman H. N. et al. Femtosecond X-ray protein nanocrystallography. Nature 470, 73–77 (2011). - PMC - PubMed
    1. Boutet S. et al. High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography. Science 337, 362–364 (2012). - PMC - PubMed
    1. Liu W. et al. Serial Femtosecond Crystallography of G Protein-Coupled Receptors. Science 342, 1521–1524 (2013). - PMC - PubMed
    1. Weierstall U. et al. Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography. Nat. Commun. 5, 3309 (2014). - PMC - PubMed
    1. Fenalti G. et al. Structural basis for bifunctional peptide recognition at human δ-opioid receptor. Nat. Struct. Mol. Biol. 22, 265–268 (2015). - PMC - PubMed

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