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Title: De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure [A potent binary mosquito larvicide revealed by de novo phasing with an X-ray free-electron laser]

Abstract

BinAB is a naturally occurring paracrystalline larvicide distributed worldwide to combat the devastating diseases borne by mosquitoes. These crystals are composed of homologous molecules, BinA and BinB, which play distinct roles in the multi-step intoxication process, transforming from harmless, robust crystals, to soluble protoxin heterodimers, to internalized mature toxin, and finally to toxic oligomeric pores. The small size of the crystals—50 unit cells per edge, on average—has impeded structural characterization by conventional means. Here we report the structure of Lysinibacillus sphaericus BinAB solved de novo by serial-femtosecond crystallography at an X-ray free-electron laser. The structure reveals tyrosine- and carboxylate-mediated contacts acting as pH switches to release soluble protoxin in the alkaline larval midgut. An enormous heterodimeric interface appears to be responsible for anchoring BinA to receptor-bound BinB for co-internalization. Furthermore, this interface is largely composed of propeptides, suggesting that proteolytic maturation would trigger dissociation of the heterodimer and progression to pore formation.

Authors:
 [1];  [2];  [2];  [2];  [2];  [3];  [3];  [4];  [1];  [5];  [5];  [5];  [5];  [5];  [5];  [5];  [5];  [6];  [7];  [6] more »;  [7];  [4];  [3];  [2] « less
  1. Univ. Grenoble Alpes, CEA, CNRS, Grenoble (France)
  2. Univ. of California, Los Angeles, CA (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. Univ. of California, Riverside, CA (United States)
  5. SLAC National Accelerator Lab., Menlo Park, CA (United States)
  6. Univ. of California, Riverside, CA (United States); California Baptist Univ., Riverside, CA (United States)
  7. Stanford Univ., Stanford, CA (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1350536
Grant/Contract Number:
AC02-76SF00515; AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Nature (London)
Additional Journal Information:
Journal Name: Nature (London); Journal Volume: 539; Journal Issue: 7627; Journal ID: ISSN 0028-0836
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND TECHNOLOGY; 60 APPLIED LIFE SCIENCES; environmental biotechnology; protein delivery; nanocrystallography

Citation Formats

Colletier, Jacques -Philippe, Sawaya, Michael R., Gingery, Mari, Rodriguez, Jose A., Cascio, Duilio, Brewster, Aaron S., Michels-Clark, Tara, Hice, Robert H., Coquelle, Nicolas, Boutet, Sébastien, Williams, Garth J., Messerschmidt, Marc, DePonte, Daniel P., Sierra, Raymond G., Laksmono, Hartawan, Koglin, Jason E., Hunter, Mark S., Park, Hyun -Woo, Uervirojnangkoorn, Monarin, Bideshi, Dennis K., Brunger, Axel T., Federici, Brian A., Sauter, Nicholas K., and Eisenberg, David S.. De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure [A potent binary mosquito larvicide revealed by de novo phasing with an X-ray free-electron laser]. United States: N. p., 2016. Web. doi:10.1038/nature19825.
Colletier, Jacques -Philippe, Sawaya, Michael R., Gingery, Mari, Rodriguez, Jose A., Cascio, Duilio, Brewster, Aaron S., Michels-Clark, Tara, Hice, Robert H., Coquelle, Nicolas, Boutet, Sébastien, Williams, Garth J., Messerschmidt, Marc, DePonte, Daniel P., Sierra, Raymond G., Laksmono, Hartawan, Koglin, Jason E., Hunter, Mark S., Park, Hyun -Woo, Uervirojnangkoorn, Monarin, Bideshi, Dennis K., Brunger, Axel T., Federici, Brian A., Sauter, Nicholas K., & Eisenberg, David S.. De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure [A potent binary mosquito larvicide revealed by de novo phasing with an X-ray free-electron laser]. United States. doi:10.1038/nature19825.
Colletier, Jacques -Philippe, Sawaya, Michael R., Gingery, Mari, Rodriguez, Jose A., Cascio, Duilio, Brewster, Aaron S., Michels-Clark, Tara, Hice, Robert H., Coquelle, Nicolas, Boutet, Sébastien, Williams, Garth J., Messerschmidt, Marc, DePonte, Daniel P., Sierra, Raymond G., Laksmono, Hartawan, Koglin, Jason E., Hunter, Mark S., Park, Hyun -Woo, Uervirojnangkoorn, Monarin, Bideshi, Dennis K., Brunger, Axel T., Federici, Brian A., Sauter, Nicholas K., and Eisenberg, David S.. 2016. "De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure [A potent binary mosquito larvicide revealed by de novo phasing with an X-ray free-electron laser]". United States. doi:10.1038/nature19825. https://www.osti.gov/servlets/purl/1350536.
@article{osti_1350536,
title = {De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure [A potent binary mosquito larvicide revealed by de novo phasing with an X-ray free-electron laser]},
author = {Colletier, Jacques -Philippe and Sawaya, Michael R. and Gingery, Mari and Rodriguez, Jose A. and Cascio, Duilio and Brewster, Aaron S. and Michels-Clark, Tara and Hice, Robert H. and Coquelle, Nicolas and Boutet, Sébastien and Williams, Garth J. and Messerschmidt, Marc and DePonte, Daniel P. and Sierra, Raymond G. and Laksmono, Hartawan and Koglin, Jason E. and Hunter, Mark S. and Park, Hyun -Woo and Uervirojnangkoorn, Monarin and Bideshi, Dennis K. and Brunger, Axel T. and Federici, Brian A. and Sauter, Nicholas K. and Eisenberg, David S.},
abstractNote = {BinAB is a naturally occurring paracrystalline larvicide distributed worldwide to combat the devastating diseases borne by mosquitoes. These crystals are composed of homologous molecules, BinA and BinB, which play distinct roles in the multi-step intoxication process, transforming from harmless, robust crystals, to soluble protoxin heterodimers, to internalized mature toxin, and finally to toxic oligomeric pores. The small size of the crystals—50 unit cells per edge, on average—has impeded structural characterization by conventional means. Here we report the structure of Lysinibacillus sphaericus BinAB solved de novo by serial-femtosecond crystallography at an X-ray free-electron laser. The structure reveals tyrosine- and carboxylate-mediated contacts acting as pH switches to release soluble protoxin in the alkaline larval midgut. An enormous heterodimeric interface appears to be responsible for anchoring BinA to receptor-bound BinB for co-internalization. Furthermore, this interface is largely composed of propeptides, suggesting that proteolytic maturation would trigger dissociation of the heterodimer and progression to pore formation.},
doi = {10.1038/nature19825},
journal = {Nature (London)},
number = 7627,
volume = 539,
place = {United States},
year = 2016,
month = 9
}

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  • BinAB is a naturally occurring paracrystalline larvicide distributed worldwide to combat the devastating diseases borne by mosquitoes. These crystals are composed of homologous molecules, BinA and BinB, which play distinct roles in the multi-step intoxication process, transforming from harmless, robust crystals, to soluble protoxin heterodimers, to internalized mature toxin, and finally to toxic oligomeric pores. The small size of the crystals - 50 unit cells per edge, on average - has impeded structural characterization by conventional means. Here we report the structure of Lysinibacillus sphaericus BinAB solved de novo by serial-femtosecond crystallography at an X-ray free-electron laser. The structure revealsmore » tyrosine- and carboxylate-mediated contacts acting as pH switches to release soluble protoxin in the alkaline larval midgut. An enormous heterodimeric interface appears to be responsible for anchoring BinA to receptor-bound BinB for co-internalization. Remarkably, this interface is largely composed of propeptides, suggesting that proteolytic maturation would trigger dissociation of the heterodimer and progression to pore formation.« less
  • Structural information about biological macromolecules near the atomic scale provides important insight into the functions of these molecules. To date, X-ray crystallography has been the predominant method used for macromolecular structure determination. However, challenges exist when solving structures with X-rays, including the phase problem and radiation damage. X-ray-free electron lasers (X-ray FELs) have enabled collection of diffraction information before the onset of radiation damage, yet the majority of structures solved at X-ray FELs have been phased using external information via molecular replacement. De novo phasing at X-ray FELs has proven challenging due in part to per-pulse variations in intensity andmore » wavelength. Here we report the solution of a selenobiotinyl-streptavidin structure using phases obtained by the anomalous diffraction of selenium measured at a single wavelength (Se-SAD) at the Linac Coherent Light Source. Finally, our results demonstrate Se-SAD, routinely employed at synchrotrons for novel structure determination, is now possible at X-ray FELs.« less
  • Structural information about biological macromolecules near the atomic scale provides important insight into the functions of these molecules. To date, X-ray crystallography has been the predominant method used for macromolecular structure determination. But, challenges exist when solving structures with X-rays, including the phase problem and radiation damage. X-ray-free electron lasers (X-ray FELs) have enabled collection of diffraction information before the onset of radiation damage, yet the majority of structures solved at X-ray FELs have been phased using external information via molecular replacement. De novo phasing at X-ray FELs has proven challenging due in part to per-pulse variations in intensity andmore » wavelength. We report the solution of a selenobiotinyl-streptavidin structure using phases obtained by the anomalous diffraction of selenium measured at a single wavelength (Se-SAD) at the Linac Coherent Light Source. These results demonstrate Se-SAD, routinely employed at synchrotrons for novel structure determination, is now possible at X-ray FELs.« less
  • Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) offers unprecedented possibilities for macromolecular structure determination of systems that are prone to radiation damage. However, phasing XFEL data de novo is complicated by the inherent inaccuracy of SFX data, and only a few successful examples, mostly based on exceedingly strong anomalous or isomorphous difference signals, have been reported. Here, it is shown that SFX data from thaumatin microcrystals can be successfully phased using only the weak anomalous scattering from the endogenous S atoms. Furthermore, a step-by-step investigation is presented of the particular problems of SAD phasing of SFX data, analysingmore » data from a derivative with a strong anomalous signal as well as the weak signal from endogenous S atoms.« less