Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data

Nature Communications

Volumn 6, Issue , 2015, Pages

  Ginn, Helen M ^a   Messerschmidt, Marc ^b,f   Ji, Xiaoyun ^a,c   Zhang, Hanwen ^a   Axford, Danny ^d   Gildea, Richard J ^d   Winter, Graeme ^d   Brewster, Aaron S ^e   Hattne, Johan ^e   Wagner, Armin ^d   Grimes, Jonathan M ^a,d   Evans, Gwyndaf ^d   Sauter, Nicholas K ^e   Sutton, Geoff ^a   Stuart, David I ^a,d  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

^c YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d Diamond House Diamond Light Source Harwell Science and Innovation Campus ^*  (United Kingdom)

^e LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^f NATIONAL SCIENCE FOUNDATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CPV17 POLYHEDRIN; POLYHEDRIN; UNCLASSIFIED DRUG; VIRAL PROTEIN;

CRYSTALLOGRAPHY; DATA SET; ELECTRON; ESTIMATION METHOD; PHENOTYPE; PROTEIN; TEMPERATURE EFFECT;

ARTICLE; CRYSTAL; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; CYPOVIRUS; EVOLUTION; LASER; PHENOTYPE; PHYSICAL MODEL; PROTEIN STRUCTURE; ROOM TEMPERATURE; SERIAL FEMTOSECOND CRYSTALLOGRAPHY; SYNCHROTRON; X RAY DIFFRACTION; X RAY FREE ELECTRON LASER; ANIMAL; CHEMISTRY; GENE VECTOR; GENETICS; IMAGE PROCESSING; MOLECULAR MODEL; MOSQUITO; PROCEDURES; PROTEIN CONFORMATION; REOVIRIDAE; VIROLOGY;

CYPOVIRUS;

ANIMALS; CRYSTALLOGRAPHY; CULICIDAE; GENETIC VECTORS; IMAGE PROCESSING, COMPUTER-ASSISTED; MODELS, MOLECULAR; PROTEIN CONFORMATION; REOVIRIDAE; VIRAL STRUCTURAL PROTEINS;

EID: 84924386737     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms7435     Document Type: Article

References (43)

1. Kunimi, Y. Current status and prospects on microbial control in Japan. J. Invertebr. Pathol. 95, 181-186 (2007).
2. Goldsmith, M. R., Shimada, T. & Abe, H. The genetics and genomics of the silkworm, bombyx mori. Annu. Rev. Entomol. 50, 71-100 (2005).
3. Poinar, Jr. G. & Poinar, R. Fossil evidence of insect pathogens. J. Invertebr. Pathol. 89, 243-250 (2005).
4. Coulibaly, F. et al. The molecular organization of cypovirus polyhedra. Nature 446, 97-101 (2007).
5. Ji, X. et al. How baculovirus polyhedra fit square pegs into round holes to robustly package viruses. EMBO J. 29, 505-514 (2010).
6. Axford, D., Ji, X., Stuart, D. I. & Sutton, G. In cellulo structure determination of a novel cypovirus polyhedrin. Acta Crystallogr. D Biol. Crystallogr. 70, 1435-1441 (2014).
7. Chapman, H. N. et al. Femtosecond X-ray protein nanocrystallography. Nature 470, 73-77 (2011).
8. Redecke, L. et al. Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser. Science 339, 227-230 (2013).
9. Liu, W. et al. Serial femtosecond crystallography of G protein-coupled receptors. Science 342, 1521-1524 (2013).
10. Boutet, S. et al. High-resolution protein structure determination by serial femtosecond crystallography. Science 337, 362-364 (2012).
11. Tenboer, J. et al. Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein. Science 346, 1242-1246 (2014).
12. White, T. A. Post-refinement method for snapshot serial crystallography. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 369, 20130330 (2014).
13. Kabsch, W. Processing of X-ray snapshots from crystals in random orientations. Acta Crystallogr. Sect. D Biol. Crystallogr. 70, 2204-2216 (2014).
14. DePonte, D. P. et al. Gas dynamic virtual nozzle for generation of microscopic droplet streams. J. Phys. D Appl. Phys. 41, 195505 (2008).
15. Sauter, N. K., Hattne, J., Grosse-Kunstleve, R. W. & Echols, N. New Pythonbased methods for data processing. Acta Crystallogr. D Biol. Crystallogr. 69, 1274-1282 (2013).
16. Hattne, J. et al. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. Nat. Methods 11, 545-548 (2014).
17. Greenhough, T. J. & Helliwell, J. R. Oscillation camera data processing: Reflecting range and prediction of partiality. 2. Monochromatized synchrotron X-radiation from a singly bent triangular monochromator. J. Appl. Crystallogr. 15, 493-508 (1982).
18. Kabsch, W. Integration, scaling, space-group assignment and post-refinement. Acta Crystallogr. Sect. D Biol. Crystallogr. 66, 133-144 (2010).
19. Barends, T. R. et al. De novo protein crystal structure determination from X-ray free-electron laser data. Nature 505, 244-247 (2014).
20. Margaritondo, G. & Rebernik Ribic, P. A simplified description of X-ray free-electron lasers. J. Synchrotron. Radiat. 18, 101-108 (2011).
21. Waterman, D. G. et al. The DIALS framework for integration software. CCP4 Newsletter on Protein Crystallography 49, 16-19 (2013).
22. Rossmann, M. G., Leslie, A. G. W., Abdel-Meguid, S. S. & Tsukihara, T. Processing and post-refinement of oscillation camera data. J. Appl. Cryst. 12, 570-581 (1979).
23. Karplus, P. A. & Diederichs, K. Linking crystallographic model and data quality. Science 336, 1030-1033 (2012).
24. Brehm, W. & Diederichs, K. Breaking the indexing ambiguity in serial crystallography. Acta Crystallogr. D Biol. Crystallogr. 70, 101-109 (2014).
25. Gildea, R. J. et al. New methods for indexing multi-lattice diffraction data. Acta Crystallogr. D Biol. Crystallogr. 70, 2652-2666.
26. Anduleit, K. et al. Crystal lattice as biological phenotype for insect viruses. Protein Sci. 14, 2741-2743 (2005).
27. Rohrmann, G. F. Polyhedrin structure. J. Gen. Virol. 67, 1499-1513 (1986).
28. Donovan, J. W. & White, T. M. Alkaline hydrolysis of the disulfide bonds of ovomucoid and of low molecular weight aliphatic and aromatic disulfides. Biochemistry 10, 32-38 (1971).
29. Juers, D. H. & Matthews, B. W. Reversible lattice repacking illustrates the temperature dependence of macromolecular interactions. J. Mol. Biol. 311, 851-862 (2001).
30. Weierstall, U. et al. Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography. Nat. Commun. 5, 3309 (2014).
31. Shapiro, A. et al. Morphological and molecular characterization of a Cypovirus (Reoviridae) from the mosquito Uranotaenia sapphirina (Diptera: Culicidae). J. Virol. 79, 9430-9438 (2005).
32. Zhao, Y., Chapman, D. A. & Jones, I. M. Improving baculovirus recombination. Nucleic Acids Res. 31, E6-E6 (2003).
33. Emma, P. et al. First lasing and operation of an ångstrom-wavelength free-electron laser. Nat. Photon. 4, 641-647 (2010).
34. Lomb, L. et al. An anti-settling sample delivery instrument for serial femtosecond crystallography. J. Appl. Crystallogr. 45, 674-678 (2012).
35. Watson, H. C., Shotton, D. M., Cox, J. M. & Muirhead, H. Three-dimensional Fourier synthesis of tosyl-elastase at 3.5Å resolution. Nature 225, 806-811 (1970).
36. Liu, D. C. & Nocedal, J. On the limited memory BFGS method for large scale optimization. Math. Program. B 45, 503-528 (1989).
37. Murshudov, G. N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 67, 355-367 (2011).
38. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674 (2007).
39. Emsley, P. & Cowtan, K. Coot: Model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132 (2004).
40. Cowtan, K. The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr. D Biol. Crystallogr. 62, 1002-1011 (2006).
41. Adams, P. D. et al. PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213-221 (2010).
42. Maia, F. R. The Coherent X-ray Imaging Data Bank. Nat. Methods 9, 854-855 (2012).
43. Stuart, D. I., Levine, M., Muirhead, H. & Stammers, D. K. Crystal structure of cat muscle pyruvate kinase at a resolution of 2.6Å. J. Mol. Biol. 134, 109-142 (1979).