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The protein complex crystallography beamline (BL19U1) at the Shanghai Synchrotron Radiation Facility

  • Wei-Zhe Zhang
  • Jian-Chao Tang
  • Si-Sheng Wang
  • Zhi-Jun Wang
  • Wen-Ming QinEmail author
  • Jian-Hua HeEmail author
Article
  • 53 Downloads

Abstract

The protein complex crystallographic beamline BL19U1 at the Shanghai Synchrotron Radiation Facility is one of the five beamlines dedicated to protein sciences operated by National Facility for Protein Science (Shanghai, China). The beamline, which features a small-gap in-vacuum undulator, has been officially open to users since March 2015. This beamline delivers X-ray in the energy range 7–15 keV. With its high flux, low divergence beam and a large active area detector, BL19U1 is designed for proteins with large molecular weight and large crystallographic unit cell dimensions. Good performance and stable operation of the beamline have allowed the number of Protein Data Bank (PDB) depositions and the number of articles published based on data collected at this beamline to increase steadily. To date, over 300 research groups have collected data at the beamline. More than 600 PDB entries have been deposited at the PDB (www.pdb.org). More than 300 papers have been published that include data collected at the beamline, including 21 research articles published in the top-level journals Cell, Nature, and Science.

Keywords

MX beamlines Macromolecular crystallography Shanghai Synchrotron Radiation Facility SSRF-BL19U1 

Notes

Acknowledgements

We thank the staff of the SSRF MX team for design, installation, and continuing collaboration, along with the assistance of the SSRF research support groups.

References

  1. 1.
    S.E. Thomas, V. Mendes, S.Y. Kim et al., Structural biology and the design of new therapeutics: from HIV and cancer to mycobacterial infections—a paper dedicated to John Kendrew. J. Mol. Biol. 429(17), 2677–2693 (2017).  https://doi.org/10.1016/j.jmb.2017.06.014 CrossRefGoogle Scholar
  2. 2.
    D.C. Wang, Structural biology in China. Prog. Biochem. Biophys. 41(10), 944–971 (2014).  https://doi.org/10.3724/Sp.J.1206.2014.00240 CrossRefGoogle Scholar
  3. 3.
    M. Jiang, X. Yang, H. Xu et al., Shanghai Synchrotron Radiation Facility. Chin. Sci. Bull. 54(22), 4171 (2009).  https://doi.org/10.1007/s11434-009-0689-y CrossRefGoogle Scholar
  4. 4.
    R.L. Owen, J. Juanhuix, M. Fuchs, Current advances in synchrotron radiation instrumentation for MX experiments. Arch. Biochem. Biophys. 602, 21–31 (2016).  https://doi.org/10.1016/j.abb.2016.03.021 CrossRefGoogle Scholar
  5. 5.
    W.R. Wikoff, W. Schildkamp, J.E. Johnson, Increased resolution data from a large unit cell crystal collected at a third-generation synchrotron X-ray source. Acta Crystallogr. Sect. D 56(7), 890–893 (2000).  https://doi.org/10.1107/S0907444900005941 CrossRefGoogle Scholar
  6. 6.
    N. Li, X. Li, Y. Wang et al., The new NCPSS BL19U2 beamline at the SSRF for small-angle X-ray scattering from biological macromolecules in solution. J. Appl. Crystallogr. 49(Pt 5), 1428–1432 (2016).  https://doi.org/10.1107/S160057671601195X CrossRefGoogle Scholar
  7. 7.
    H. Qin, Y. Zhao, N. Wang et al., Layout and operation of the undulator canted beamlines on BL19U at SSRF. Nucl. Tech. 39(11), 110101 (2016).  https://doi.org/10.11889/j.0253-3219.2016.hjs.39.110101. (in Chinese) CrossRefGoogle Scholar
  8. 8.
    A. Perrakis, F. Cipriani, J.C. Castagna et al., Protein microcrystals and the design of a microdiffractometer: current experience and plans at EMBL and ESRF/ID13. Acta Crystallogr. D Biol. Crystallogr. 55(Pt 10), 1765–1770 (1999).  https://doi.org/10.1107/s0907444999009348 CrossRefGoogle Scholar
  9. 9.
    T. Loeliger, C. Bronnimann, T. Donath, et al., The new PILATUS3 ASIC with instant retrigger capability, in: 2012 IEEE Nuclear Science Symposium and Medical Imaging Conference Record (Nss/Mic) (2012), pp. 610–615.  https://doi.org/10.1109/nssmic.2012.6551180
  10. 10.
    T.M. McPhillips, S.E. McPhillips, H.-J. Chiu et al., Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines. J. Synchrotron Radiat. 9(6), 401–406 (2002).  https://doi.org/10.1107/S0909049502015170 CrossRefGoogle Scholar
  11. 11.
    Q. Wang, S. Huang, B. Sun et al., Control and data acquisition system for the macromolecular crystallography beamline of SSRF. Nucl. Tech. 35, 5–11 (2012). (in Chinese) Google Scholar
  12. 12.
    Q.S. Wang, K.H. Zhang, Y. Cui et al., Upgrade of macromolecular crystallography beamline BL17U1at SSRF. Nucl. Sci. Tech. 29, 68 (2018).  https://doi.org/10.1007/s41365-018-0398-9 CrossRefGoogle Scholar
  13. 13.
    P. Liu, Y.N. Zhou, Q.R. Mi et al., EPICS-based data acquisition system on beamlines at SSRF. Nucl. Tech. 33, 415–419 (2010). (in Chinese) Google Scholar
  14. 14.
    W. Minor, M. Cymborowski, Z. Otwinowski et al., HKL-3000: the integration of data reduction and structure solution—from diffraction images to an initial model in minutes. Acta Crystallogr. D 62(8), 859–866 (2006).  https://doi.org/10.1107/S0907444906019949 CrossRefGoogle Scholar
  15. 15.
    W. Kabsch, Automatic indexing of rotation diffraction patterns. J. Appl. Crystallogr. 21(1), 67–72 (1988).  https://doi.org/10.1107/S0021889887009737 CrossRefGoogle Scholar
  16. 16.
    M.D. Winn, C.C. Ballard, K.D. Cowtan et al., Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67(Pt 4), 235–242 (2011).  https://doi.org/10.1107/S0907444910045749 CrossRefGoogle Scholar
  17. 17.
    P.D. Adams, P.V. Afonine, G. Bunkoczi et al., PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66(Pt 2), 213–221 (2010).  https://doi.org/10.1107/S0907444909052925 CrossRefGoogle Scholar
  18. 18.
    G.M. Sheldrick, A short history of SHELX. Acta Crystallogr. A 64(1), 112–122 (2008)CrossRefGoogle Scholar
  19. 19.
    X. Wang, J. Feng, Y. Xue et al., Structural basis of N(6)-adenosine methylation by the METTL3–METTL14 complex. Nature 534(7608), 575–578 (2016).  https://doi.org/10.1038/nature18298 CrossRefGoogle Scholar
  20. 20.
    J. Wang, J. Li, H. Zhao et al., Structural and mechanistic basis of PAM-dependent spacer acquisition in CRISPR–Cas systems. Cell 163(4), 840–853 (2015).  https://doi.org/10.1016/j.cell.2015.10.008 CrossRefGoogle Scholar
  21. 21.
    L. Hu, J. Lu, J. Cheng et al., Structural insight into substrate preference for TET-mediated oxidation. Nature 527, 118 (2015).  https://doi.org/10.1038/nature15713 CrossRefGoogle Scholar
  22. 22.
    H. Wang, Y. Shi, J. Song et al., ebola viral glycoprotein bound to its endosomal receptor Niemann-Pick C1. Cell 164(1–2), 258–268 (2016).  https://doi.org/10.1016/j.cell.2015.12.044 CrossRefGoogle Scholar
  23. 23.
    Y. Li, J. Han, Y. Zhang et al., Structural basis for activity regulation of MLL family methyltransferases. Nature 530(7591), 447–452 (2016).  https://doi.org/10.1038/nature16952 CrossRefGoogle Scholar
  24. 24.
    J. Ding, K. Wang, W. Liu et al., Pore-forming activity and structural autoinhibition of the gasdermin family. Nature 535(7610), 111–116 (2016).  https://doi.org/10.1038/nature18590 CrossRefGoogle Scholar
  25. 25.
    M. Zeng, Y. Shang, Y. Araki et al., Phase transition in postsynaptic densities underlies formation of synaptic complexes and synaptic plasticity. Cell 166(5), 1163–1175e12 (2016).  https://doi.org/10.1016/j.cell.2016.07.008 CrossRefGoogle Scholar
  26. 26.
    L. Liu, X. Li, J. Wang et al., Two distant catalytic sites are responsible for C2c2 RNase activities. Cell 168(1–2), 121–134e12 (2017).  https://doi.org/10.1016/j.cell.2016.12.031 CrossRefGoogle Scholar
  27. 27.
    D. Dong, M. Guo, S. Wang et al., Structural basis of CRISPR–SpyCas9 inhibition by an anti-CRISPR protein. Nature 546(7658), 436–439 (2017).  https://doi.org/10.1038/nature22377 CrossRefGoogle Scholar
  28. 28.
    L. Liu, X. Li, J. Ma et al., The molecular architecture for RNA-guided RNA cleavage by Cas13a. Cell 170(4), 714–726e10 (2017).  https://doi.org/10.1016/j.cell.2017.06.050 CrossRefGoogle Scholar
  29. 29.
    H. Li, R. Liefke, J. Jiang et al., Polycomb-like proteins link the PRC2 complex to CpG islands. Nature 549(7671), 287–291 (2017).  https://doi.org/10.1038/nature23881 CrossRefGoogle Scholar
  30. 30.
    H. Chen, J. Xue, D. Churikov et al., Structural insights into yeast telomerase recruitment to telomeres. Cell 172(1–2), 331–343e13 (2018).  https://doi.org/10.1016/j.cell.2017.12.008 CrossRefGoogle Scholar
  31. 31.
    Y. Wang, M. Shi, H. Feng et al., Structural insights into non-canonical ubiquitination catalyzed by SidE. Cell 173(5), 1231–1243e16 (2018).  https://doi.org/10.1016/j.cell.2018.04.023 CrossRefGoogle Scholar
  32. 32.
    M. Mompean, W. Li, J. Li et al., The structure of the necrosome RIPK1–RIPK3 core, a human hetero-amyloid signaling complex. Cell 173(5), 1244–1253e10 (2018).  https://doi.org/10.1016/j.cell.2018.03.032 CrossRefGoogle Scholar
  33. 33.
    Y. Dong, Y. Mu, Y. Xie et al., Structural basis of ubiquitin modification by the Legionella effector SdeA. Nature 557(7707), 674–678 (2018).  https://doi.org/10.1038/s41586-018-0146-7 CrossRefGoogle Scholar
  34. 34.
    Y. Yan, Q. Liu, X. Zang et al., Resistance-gene-directed discovery of a natural-product herbicide with a new mode of action. Nature 559(7714), 415–418 (2018).  https://doi.org/10.1038/s41586-018-0319-4 CrossRefGoogle Scholar
  35. 35.
    L. Zhang, A. Serra-Cardona, H. Zhou et al., Multisite substrate recognition in Asf1-dependent acetylation of histone H3 K56 by Rtt109. Cell 174(4), 818–830e11 (2018).  https://doi.org/10.1016/j.cell.2018.07.005 CrossRefGoogle Scholar
  36. 36.
    P. Zhou, Y. She, N. Dong et al., Alpha-kinase 1 is a cytosolic innate immune receptor for bacterial ADP-heptose. Nature 561(7721), 122–126 (2018).  https://doi.org/10.1038/s41586-018-0433-3 CrossRefGoogle Scholar
  37. 37.
    L. You, J. Ma, J. Wang et al., Structure studies of the CRISPR–Csm complex reveal mechanism of co-transcriptional interference. Cell 176(1–2), 239–253e16 (2019).  https://doi.org/10.1016/j.cell.2018.10.052 CrossRefGoogle Scholar
  38. 38.
    B. Zhang, J. Li, X. Yang et al., Crystal structures of membrane transporter MmpL3, an anti-TB drug target. Cell 176(3), 636–648e13 (2019).  https://doi.org/10.1016/j.cell.2019.01.003 CrossRefGoogle Scholar
  39. 39.
    H. Song, Z. Zhao, Y. Chai et al., Molecular basis of arthritogenic alphavirus receptor MXRA8 binding to Chikungunya virus envelope protein. Cell 177(7), 1714–1724e13 (2019).  https://doi.org/10.1016/j.cell.2019.04.008 CrossRefGoogle Scholar
  40. 40.
    H. Song, J. Qi, H. Xiao et al., Avian-to-human receptor-binding adaptation by Influenza A Virus Hemagglutinin H4. Cell Rep. 20(5), 1201–1214 (2017).  https://doi.org/10.1016/j.celrep.2017.07.028 CrossRefGoogle Scholar
  41. 41.
    W. Tian, P. Yan, N. Xu et al., The HRP3 PWWP domain recognizes the minor groove of double-stranded DNA and recruits HRP3 to chromatin. Nucleic Acids Res. 47(10), 5436–5448 (2019).  https://doi.org/10.1093/nar/gkz294 CrossRefGoogle Scholar
  42. 42.
    H. Liu, F. Shen, P. Haruehanroengra et al., A DNA structure containing Ag(I)-mediated G:G and C:C base pairs. Angew. Chem. Int. Ed. Engl. 56(32), 9430–9434 (2017).  https://doi.org/10.1002/anie.201704891 CrossRefGoogle Scholar
  43. 43.
    T. Xu, C.-Z. Zhou, J. Xiao et al., Unique conformation in a natural interruption sequence of type XIX collagen revealed by its high-resolution crystal structure. Biochemistry 57(7), 1087–1095 (2018).  https://doi.org/10.1021/acs.biochem.7b01010 CrossRefGoogle Scholar
  44. 44.
    J.X. Yao, ACORN in CCP4 and its applications. Acta Crystallogr. A 58(11), 1941–1947 (2002).  https://doi.org/10.1107/S0907444902016621 CrossRefGoogle Scholar

Copyright information

© China Science Publishing & Media Ltd. (Science Press), Shanghai Institute of Applied Physics, the Chinese Academy of Sciences, Chinese Nuclear Society and Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  1. 1.National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute (Zhangjiang Laboratory)Chinese Academy of SciencesShanghaiChina
  2. 2.Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute (Zhangjiang Laboratory)Chinese Academy of SciencesShanghaiChina

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