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Native phasing of x-ray free-electron laser data for a G protein–coupled receptor

Journal Article · · Science Advances
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  1. Univ. of Zurich (Switzerland); DOE/OSTI
  2. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)
  3. Univ. of Southern California, Los Angeles, CA (United States)
  4. Moscow Inst. of Physics and Technology (MIPT), Dolgoprudny (Russian Federation); Univ. of Southern California, Los Angeles, CA (United States)
  5. SLAC National Accelerator Lab., Menlo Park, CA (United States)
  6. Chinese Academy of Sciences (CAS), Beijing (China)
  7. ShanghaiTech Univ., Shanghai (China); Chinese Academy of Sciences (CAS), Beijing (China)
  8. Arizona State Univ., Tempe, AZ (United States)
  9. Univ. of Southern California, Los Angeles, CA (United States); Shanghai Tech. Univ. (China)

Serial femtosecond crystallography (SFX) takes advantage of extremely bright and ultrashort pulses produced by x-ray free-electron lasers (XFELs), allowing for the collection of high-resolution diffraction intensities from micrometer-sized crystals at room temperature with minimal radiation damage, using the principle of “diffraction-before-destruction.” However, de novo structure factor phase determination using XFELs has been difficult so far. We demonstrate the ability to solve the crystallographic phase problem for SFX data collected with an XFEL using the anomalous signal from native sulfur atoms, leading to a bias-free room temperature structure of the human A2Aadenosine receptor at 1.9 Å resolution. The advancement was made possible by recent improvements in SFX data analysis and the design of injectors and delivery media for streaming hydrated microcrystals. This general method should accelerate structural studies of novel difficult-to-crystallize macromolecules and their complexes.

Research Organization:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH); Ministry of Science and Technology of China; National Science Foundation (NSF), Science and Technology Center; PIER Helmholtz Graduate School; Helmholtz Association; Russian Ministry of Education and Science
Grant/Contract Number:
AC02-76SF00515
OSTI ID:
1625958
Journal Information:
Science Advances, Journal Name: Science Advances Journal Issue: 9 Vol. 2; ISSN 2375-2548
Publisher:
AAASCopyright Statement
Country of Publication:
United States
Language:
English

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  • Fukuda, Y.
  • Coherent X-ray Imaging Data Bank (Lawrence Berkeley National Laboratory); The University of Tokyo, RIKEN SPring-8 Center, POSTECH, Osaka University, Kyoto University, Japan Synchrotron Radiation Research Institute https://doi.org/10.11577/1274312
dataset January 2016
Accurate determination of segmented X-ray detector geometry journal January 2015
Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals journal March 2015

Cited By (29)

Multi-wavelength anomalous diffraction de novo phasing using a two-colour X-ray free-electron laser with wide tunability journal October 2017
Viscosity-adjustable grease matrices for serial nanocrystallography journal January 2020
Fast iodide-SAD phasing for high-throughput membrane protein structure determination text January 2017
In Silico Studies Targeting G-protein Coupled Receptors for Drug Research Against Parkinson’s Disease journal June 2018
Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons text January 2017
New approaches towards the understanding of integral membrane proteins: A structural perspective on G protein-coupled receptors: Structural Perspective on G Protein-Coupled Receptors journal June 2017
Structures of Non-rhodopsin GPCRs Elucidated Through X-Ray Crystallography book January 2017
Breakthrough in GPCR Crystallography and Its Impact on Computer-Aided Drug Design book November 2017
High-Throughput Protein Production of Membrane Proteins in Saccharomyces cerevisiae book January 2019
Climbing the Data Mountain: Processing of SFX Data book January 2018
Could the presence of sodium ion influence the accuracy and precision of the ligand-posing in the human A2A adenosine receptor orthosteric binding site using a molecular docking approach? Insights from Dockbench journal October 2018
A benchmark study of loop modeling methods applied to G protein-coupled receptors journal May 2019
Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons journal September 2017
Hydroxyethyl cellulose matrix applied to serial crystallography journal April 2017
X-ray free electron laser: opportunities for drug discovery journal November 2017
An outlook on using serial femtosecond crystallography in drug discovery journal May 2019
Materials characterization by synchrotron x-ray microprobes and nanoprobes journal June 2018
X-ray free-electron laser: opportunities for drug discovery journal July 2018
Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation journal May 2017
XFELs for structure and dynamics in biology journal May 2017
A new MR-SAD algorithm for the automatic building of protein models from low-resolution X-ray data and a poor starting model journal January 2018
High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source journal April 2019
High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source text January 2019
Synchrotron microcrystal native-SAD phasing at a low energy journal May 2019
Toward G protein-coupled receptor structure-based drug design using X-ray lasers journal October 2019
Fast iodide-SAD phasing for high-throughput membrane protein structure determination journal May 2017
Climbing the Data Mountain: Processing of SFX Data text January 2018
Role of Extracellular Loops and Membrane Lipids for Ligand Recognition in the Neuronal Adenosine Receptor Type 2A: An Enhanced Sampling Simulation Study journal October 2018
Evolutionary couplings detect side-chain interactions journal January 2019

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