An atomic model of brome mosaic virus using direct electron detection and real-space optimization
10.1038/ncomms5808
Crossref journal-article
Springer Science and Business Media LLC
Nature Communications (297)
Bibliography

Wang, Z., Hryc, C. F., Bammes, B., Afonine, P. V., Jakana, J., Chen, D.-H., Liu, X., Baker, M. L., Kao, C., Ludtke, S. J., Schmid, M. F., Adams, P. D., & Chiu, W. (2014). An atomic model of brome mosaic virus using direct electron detection and real-space optimization. Nature Communications, 5(1).

Authors 13
  1. Zhao Wang (first)
  2. Corey F. Hryc (additional)
  3. Benjamin Bammes (additional)
  4. Pavel V. Afonine (additional)
  5. Joanita Jakana (additional)
  6. Dong-Hua Chen (additional)
  7. Xiangan Liu (additional)
  8. Matthew L. Baker (additional)
  9. Cheng Kao (additional)
  10. Steven J. Ludtke (additional)
  11. Michael F. Schmid (additional)
  12. Paul D. Adams (additional)
  13. Wah Chiu (additional)
References 47 Referenced 97
  1. Baker, M. L. et al. Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modelling. Proc. Natl Acad. Sci. USA 110, 12301–12306 (2013). (10.1073/pnas.1309947110) / Proc. Natl Acad. Sci. USA by ML Baker (2013)
  2. Li, X. et al. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat. Methods 10, 584–590 (2013). (10.1038/nmeth.2472) / Nat. Methods by X Li (2013)
  3. Bai, X. C., Fernandez, I. S., McMullan, G. & Scheres, S. H. Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles. Elife 2, e00461 (2013). (10.7554/eLife.00461) / Elife by XC Bai (2013)
  4. Henderson, R. Avoiding the pitfalls of single particle cryo-electron microscopy: Einstein from noise. Proc. Natl Acad. Sci. USA 110, 18037–18041 (2013). (10.1073/pnas.1314449110) / Proc. Natl Acad. Sci. USA by R Henderson (2013)
  5. Chen, S. et al. High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy. Ultramicroscopy 135C, 24–35 (2013). (10.1016/j.ultramic.2013.06.004) / Ultramicroscopy by S Chen (2013)
  6. Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010). (10.1107/S0907444909042073) / Acta Crystallogr. D Biol. Crystallogr. by VB Chen (2010)
  7. Johnson, J. E. & Fisher, A. J. inEncyclopedia of Virology eds Webster R., Granoff. A. 1573–1586Academic Press (1994).
  8. Lucas, R. W., Larson, S. B. & McPherson, A. The crystallographic structure of brome mosaic virus. J. Mol. Biol. 317, 95–108 (2002). (10.1006/jmbi.2001.5389) / J. Mol. Biol. by RW Lucas (2002)
  9. Zhang, R. et al. 4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus. EMBO J. 30, 3854–3863 (2011). (10.1038/emboj.2011.261) / EMBO J. by R Zhang (2011)
  10. Zhang, J. et al. Mechanism of folding chamber closure in a group II chaperonin. Nature 463, 379–383 (2010). (10.1038/nature08701) / Nature by J Zhang (2010)
  11. Milazzo, A. C. et al. Initial evaluation of a direct detection device detector for single particle cryo-electron microscopy. J. Struct. Biol. 176, 404–408 (2011). (10.1016/j.jsb.2011.09.002) / J. Struct. Biol. by AC Milazzo (2011)
  12. Bammes, B. E., Rochat, R. H., Jakana, J., Chen, D. H. & Chiu, W. Direct electron detection yields cryo-EM reconstructions at resolutions beyond 3/4 Nyquist frequency. J. Struct. Biol. 177, 589–601 (2012). (10.1016/j.jsb.2012.01.008) / J. Struct. Biol. by BE Bammes (2012)
  13. Ruskin, R. S., Yu, Z. & Grigorieff, N. Quantitative characterization of electron detectors for transmission electron microscopy. J. Struct. Biol. 184, 385–393 (2013). (10.1016/j.jsb.2013.10.016) / J. Struct. Biol. by RS Ruskin (2013)
  14. Campbell, M. G. et al. Movies of ice-embedded particles enhance resolution in electron cryo-microscopy. Structure 20, 1823–1828 (2012). (10.1016/j.str.2012.08.026) / Structure by MG Campbell (2012)
  15. McMullan, G., Clark, A. T., Turchetta, R. & Faruqi, A. R. Enhanced imaging in low dose electron microscopy using electron counting. Ultramicroscopy 109, 1411–1416 (2009). (10.1016/j.ultramic.2009.07.004) / Ultramicroscopy by G McMullan (2009)
  16. Jin, L. et al. Applications of direct detection device in transmission electron microscopy. J. Struct. Biol. 161, 352–358 (2008). (10.1016/j.jsb.2007.10.007) / J. Struct. Biol. by L Jin (2008)
  17. Glaeser, R. M., McMullan, G., Faruqi, A. R. & Henderson, R. Images of paraffin monolayer crystals with perfect contrast: minimization of beam-induced specimen motion. Ultramicroscopy 111, 90–100 (2011). (10.1016/j.ultramic.2010.10.010) / Ultramicroscopy by RM Glaeser (2011)
  18. Brilot, A. F. et al. Beam-induced motion of vitrified specimen on holey carbon film. J. Struct. Biol. 177, 630–637 (2012). (10.1016/j.jsb.2012.02.003) / J. Struct. Biol. by AF Brilot (2012)
  19. Baker, L. A. & Rubinstein, J. L. Radiation damage in electron cryomicroscopy. Methods Enzymol. 481, 371–388 (2010). (10.1016/S0076-6879(10)81015-8) / Methods Enzymol. by LA Baker (2010)
  20. Bammes, B. E., Jakana, J., Schmid, M. F. & Chiu, W. Radiation damage effects at four specimen temperatures from 4 to 100 K. J. Struct. Biol. 169, 331–341 (2010). (10.1016/j.jsb.2009.11.001) / J. Struct. Biol. by BE Bammes (2010)
  21. Glaeser, R. M., Downing, K. H., DeRosier, D., Chiu, W. & Frank, J. Electron crystallography of biological macromolecules Oxford University Press (2007). (10.1093/oso/9780195088717.001.0001)
  22. Henderson, R. et al. Outcome of the first electron microscopy validation task force meeting. Structure 20, 205–214 (2012). (10.1016/j.str.2011.12.014) / Structure by R Henderson (2012)
  23. Scheres, S. H. & Chen, S. Prevention of overfitting in cryo-EM structure determination. Nat. Methods 9, 853–854 (2012). (10.1038/nmeth.2115) / Nat. Methods by SH Scheres (2012)
  24. Ludtke, S. J., Baldwin, P. R. & Chiu, W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128, 82–97 (1999). (10.1006/jsbi.1999.4174) / J. Struct. Biol. by SJ Ludtke (1999)
  25. Liu, X., Jiang, W., Jakana, J. & Chiu, W. Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. J. Struct. Biol. 160, 11–27 (2007). (10.1016/j.jsb.2007.06.009) / J. Struct. Biol. by X Liu (2007)
  26. Liu, X. et al. Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus. Nat. Struct. Mol. Biol. 17, 830–836 (2010). (10.1038/nsmb.1823) / Nat. Struct. Mol. Biol. by X Liu (2010)
  27. Rosenthal, P. B., Crowther, R. A. & Henderson, R. An objective criterion for resolution assessment in single-particle electron microscopy. J. Mol. Biol. 333, 743–745 (2003). (10.1016/j.jmb.2003.07.013) / J. Mol. Biol. by PB Rosenthal (2003)
  28. Saad, A. et al. Fourier amplitude decay of electron cryomicroscopic images of single particles and effects on structure determination. J. Struct. Biol. 133, 32–42 (2001). (10.1006/jsbi.2001.4330) / J. Struct. Biol. by A Saad (2001)
  29. Pintilie, G. D., Zhang, J., Goddard, T. D., Chiu, W. & Gossard, D. C. Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. J. Struct. Biol. 170, 427–438 (2010). (10.1016/j.jsb.2010.03.007) / J. Struct. Biol. by GD Pintilie (2010)
  30. Pettersen, E. F. et al. UCSF Chimera–a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004). (10.1002/jcc.20084) / J. Comput. Chem. by EF Pettersen (2004)
  31. Jiang, W., Baker, M. L., Ludtke, S. J. & Chiu, W. Bridging the information gap: computational tools for intermediate resolution structure interpretation. J. Mol. Biol. 308, 1033–1044 (2001). (10.1006/jmbi.2001.4633) / J. Mol. Biol. by W Jiang (2001)
  32. Zhou, Z. H. et al. Seeing the herpesvirus capsid at 8.5 Å. Science 288, 877–880 (2000). (10.1126/science.288.5467.877) / Science by ZH Zhou (2000)
  33. Zhang, X. et al. Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction. Proc. Natl Acad. Sci. USA 105, 1867–1872 (2008). (10.1073/pnas.0711623105) / Proc. Natl Acad. Sci. USA by X Zhang (2008)
  34. Baker, M. R., Rees, I., Ludtke, S. J., Chiu, W. & Baker, M. L. Constructing and validating initial Calpha models from subnanometer resolution density maps with pathwalking. Structure 20, 450–463 (2012). (10.1016/j.str.2012.01.008) / Structure by MR Baker (2012)
  35. Baker, M. L., Zhang, J., Ludtke, S. J. & Chiu, W. Cryo-EM of macromolecular assemblies at near-atomic resolution. Nat. Protoc. 5, 1697–1708 (2010). (10.1038/nprot.2010.126) / Nat. Protoc. by ML Baker (2010)
  36. Li, Y. & Zhang, Y. REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins 76, 665–676 (2009). (10.1002/prot.22380) / Proteins by Y Li (2009)
  37. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010). (10.1107/S0907444910007493) / Acta Crystallogr. D Biol. Crystallogr. by P Emsley (2010)
  38. Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D Biol. Crystallogr. 68, 352–367 (2012). (10.1107/S0907444912001308) / Acta Crystallogr. D Biol. Crystallogr. by PV Afonine (2012)
  39. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010). (10.1107/S0907444909052925) / Acta Crystallogr. D Biol. Crystallogr. by PD Adams (2010)
  40. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, (Pt 2): 110–119 (1991). (10.1107/S0108767390010224) / Acta Crystallogr. A by TA Jones (1991)
  41. Chapman, M. Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron-density function. Acta Crystallogr. A 51, 69–80 (1995). (10.1107/S0108767394007130) / Acta Crystallogr. A by M Chapman (1995)
  42. Berman, H. M. et al. The protein data bank. Nucleic Acids Res. 28, 235–242 (2000). (10.1093/nar/28.1.235) / Nucleic Acids Res. by HM Berman (2000)
  43. DiMaio, F., Zhang, J., Chiu, W. & Baker, D. Cryo-EM model validation using independent map reconstructions. Protein Sci. 22, 865–868 (2013). (10.1002/pro.2267) / Protein Sci. by F DiMaio (2013)
  44. Ni, P. et al. An examination of the electrostatic interactions between the N-terminal tail of the brome mosaic virus coat protein and encapsidated RNAs. J. Mol. Biol. 419, 284–300 (2012). (10.1016/j.jmb.2012.03.023) / J. Mol. Biol. by P Ni (2012)
  45. Bujarski, J. J., Nagy, P. D. & Flasinski, S. Molecular studies of genetic RNA-RNA recombination in brome mosaic virus. Adv. Virus Res. 43, 275–302 (1994). (10.1016/S0065-3527(08)60051-2) / Adv. Virus Res. by JJ Bujarski (1994)
  46. Kremer, J. R., Mastronarde, D. N. & McIntosh, J. R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71–76 (1996). (10.1006/jsbi.1996.0013) / J. Struct. Biol. by JR Kremer (1996)
  47. Baker, L. A. & R., J. L. inMethods in Enzymology Vol. 481371–388Academic Press (2010).
Dates
Type When
Created 10 years, 11 months ago (Sept. 4, 2014, 10:20 a.m.)
Deposited 1 year, 2 months ago (June 2, 2024, 2:36 a.m.)
Indexed 3 weeks, 2 days ago (July 30, 2025, 11:25 a.m.)
Issued 10 years, 11 months ago (Sept. 4, 2014)
Published 10 years, 11 months ago (Sept. 4, 2014)
Published Online 10 years, 11 months ago (Sept. 4, 2014)
Funders 0

None

@article{Wang_2014, title={An atomic model of brome mosaic virus using direct electron detection and real-space optimization}, volume={5}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/ncomms5808}, DOI={10.1038/ncomms5808}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Wang, Zhao and Hryc, Corey F. and Bammes, Benjamin and Afonine, Pavel V. and Jakana, Joanita and Chen, Dong-Hua and Liu, Xiangan and Baker, Matthew L. and Kao, Cheng and Ludtke, Steven J. and Schmid, Michael F. and Adams, Paul D. and Chiu, Wah}, year={2014}, month=sep }