The use of noncrystallographic symmetry averaging to solve structures from data affected by perfect hemihedral twinning
Jazyk angličtina Země Spojené státy americké Médium print-electronic
Typ dokumentu časopisecké články, práce podpořená grantem
PubMed
26919522
PubMed Central
PMC4774877
DOI
10.1107/s2053230x16000923
PII: S2053230X16000923
Knihovny.cz E-zdroje
- Klíčová slova
- detwinning, hemihedral perfect twinning, mask envelope, merohedral twinning, molecular replacement, noncrystallographic symmetry averaging, symmetry, twin domain, virus structure,
- MeSH
- Cercopithecus aethiops MeSH
- Kobuvirus ultrastruktura MeSH
- krystalizace MeSH
- krystalografie rentgenová MeSH
- molekulární modely MeSH
- vazba proteinů MeSH
- virion chemie ultrastruktura MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Hemihedral twinning is a crystal-growth anomaly in which a specimen is composed of two crystal domains that coincide with each other in three dimensions. However, the orientations of the crystal lattices in the two domains differ in a specific way. In diffraction data collected from hemihedrally twinned crystals, each observed intensity contains contributions from both of the domains. With perfect hemihedral twinning, the two domains have the same volumes and the observed intensities do not contain sufficient information to detwin the data. Here, the use of molecular replacement and of noncrystallographic symmetry (NCS) averaging to detwin a 2.1 Å resolution data set for Aichi virus 1 affected by perfect hemihedral twinning is described. The NCS averaging enabled the correction of errors in the detwinning introduced by the differences between the molecular-replacement model and the crystallized structure. The procedure permitted the structure to be determined from a molecular-replacement model that had 16% sequence identity and a 1.6 Å r.m.s.d. for C(α) atoms in comparison to the crystallized structure. The same approach could be used to solve other data sets affected by perfect hemihedral twinning from crystals with NCS.
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Brünger, A. T. (1992). Nature (London), 355, 472–475. PubMed
Brunger, A. T. (2007). Nature Protoc. 2, 2728–2733. PubMed
Chandra, N., Acharya, K. R. & Moody, P. C. E. (1999). Acta Cryst. D55, 1750–1758. PubMed
Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. & Richardson, D. C. (2010). Acta Cryst. D66, 12–21. PubMed PMC
Chen, Z., Blanc, E. & Chapman, M. S. (1999). Acta Cryst. D55, 219–224. PubMed
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486–501. PubMed PMC
Evans, P. (2006). Acta Cryst. D62, 72–82. PubMed
Fabiola, F., Korostelev, A. & Chapman, M. S. (2006). Acta Cryst. D62, 227–238. PubMed
Filman, D. J., Wien, M. W., Cunningham, J. A., Bergelson, J. M. & Hogle, J. M. (1998). Acta Cryst. D54, 1261–1272. PubMed
Grainger, C. T. (1969). Acta Cryst. A25, 427–434.
Helliwell, J. R. (2008). Crystallogr. Rev. 14, 189–250.
Jones, T. A., Bergdoll, M. & Kjeldgaard, M. (1990). Crystallographic and Modeling Methods in Molecular Design, edited by C. E. Bugg & S. E. Ealick, pp. 189–199. New York: Springer-Verlag.
Kabsch, W. (2010). Acta Cryst. D66, 125–132. PubMed PMC
Kleywegt, G. J. (2000). Acta Cryst. D56, 249–265. PubMed
Kleywegt, G. J. & Brünger, A. T. (1996). Structure, 4, 897–904. PubMed
Kleywegt, G. J. & Jones, T. A. (1999). Acta Cryst. D55, 941–944. PubMed
Kleywegt, G. J. & Read, R. J. (1997). Structure, 5, 1557–1569. PubMed
Krishnaswamy, S. & Rossmann, M. G. (1990). J. Mol. Biol. 211, 803–844. PubMed
Luo, M., He, C., Toth, K. S., Zhang, C. X. & Lipton, H. L. (1992). Proc. Natl Acad. Sci. USA, 89, 2409–2413. PubMed PMC
Miller, S. T., Hogle, J. M. & Filman, D. J. (2001). J. Mol. Biol. 307, 499–512. PubMed
Muckelbauer, J. K., Kremer, M., Minor, I., Tong, L., Zlotnick, A., Johnson, J. E. & Rossmann, M. G. (1995). Acta Cryst. D51, 871–887. PubMed
Padilla, J. E. & Yeates, T. O. (2003). Acta Cryst. D59, 1124–1130. PubMed
Parsons, S. (2003). Acta Cryst. D59, 1995–2003. PubMed
Plevka, P., Hafenstein, S., Harris, K. G., Cifuente, J. O., Zhang, Y., Bowman, V. D., Chipman, P. R., Bator, C. M., Lin, F., Medof, M. E. & Rossmann, M. G. (2010). J. Virol. 84, 12665–12674. PubMed PMC
Plevka, P., Kazaks, A., Voronkova, T., Kotelovica, S., Dishlers, A., Liljas, L. & Tars, K. (2009). J. Mol. Biol. 391, 635–647. PubMed
Porta, C., Kotecha, A., Burman, A., Jackson, T., Ren, J., Loureiro, S., Jones, I. M., Fry, E. E., Stuart, D. I. & Charleston, B. (2013). PLoS Pathog. 9, e1003255. PubMed PMC
Redinbo, M. R. & Yeates, T. O. (1993). Acta Cryst. D49, 375–380. PubMed
Smyth, M., Tate, J., Hoey, E., Lyons, C., Martin, S. & Stuart, D. (1995). Nature Struct. Biol. 2, 224–231. PubMed
Tong, L. & Rossmann, M. G. (1990). Acta Cryst. A46, 783–792. PubMed
Tuthill, T. J., Harlos, K., Walter, T. S., Knowles, N. J., Groppelli, E., Rowlands, D. J., Stuart, D. I. & Fry, E. E. (2009). PLoS Pathog. 5, e1000620. PubMed PMC
Vellieux, F. M. D. A. P., Hunt, J. F., Roy, S. & Read, R. J. (1995). J. Appl. Cryst. 28, 347–351.
Wang, X. et al. (2012). Nature Struct. Mol. Biol. 19, 424–429. PubMed PMC
Winn, M. D. et al. (2011). Acta Cryst. D67, 235–242. PubMed
Yamashita, T., Kobayashi, S., Sakae, K., Nakata, S., Chiba, S., Ishihara, Y. & Isomura, S. (1991). J. Infect. Dis. 164, 954–957. PubMed
Yamashita, T., Sakae, K., Tsuzuki, H., Suzuki, Y., Ishikawa, N., Takeda, N., Miyamura, T. & Yamazaki, S. (1998). J. Virol. 72, 8408–8412. PubMed PMC
Yeates, T. O. (1997). Methods Enzymol. 276, 344–358. PubMed
Yeates, T. O. & Fam, B. C. (1999). Structure, 7, R25–R29. PubMed
Structure of Aichi Virus 1 and Its Empty Particle: Clues to Kobuvirus Genome Release Mechanism