메뉴 건너뛰기




Volumn 284, Issue 5, 1998, Pages 1439-1452

Imaging RNA and dynamic protein segments with low-resolution virus crystallography: Experimental design, data processing and implications of electron density maps

Author keywords

Bacteriophage structure; Protein crystallography; Small angle scattering; Virus crystallography; Virus structure

Indexed keywords

VIRUS PROTEIN; VIRUS RNA;

EID: 0032545188     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2231     Document Type: Article
Times cited : (32)

References (42)
  • 2
    • 0030272365 scopus 로고    scopus 로고
    • Low-resolution meets high: Towards a resolution continuum from cells to atoms
    • Baker, T. S. & Johnson, J. E. (1996). Low-resolution meets high: towards a resolution continuum from cells to atoms. Curr. Opin. Struct. Biol. 6, 585-594.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 585-594
    • Baker, T.S.1    Johnson, J.E.2
  • 4
    • 0028773272 scopus 로고
    • Functional implications of quasi-equivalence in a T = 3 icosahedral animal virus established by cryo-electron microscopy and X-ray crystallography
    • Cheng, R. H., Reddy, V. S., Olson, N. H., Fisher, A. J., Baker, T. S. & Johnson, J. E. (1994). Functional implications of quasi-equivalence in a T = 3 icosahedral animal virus established by cryo-electron microscopy and X-ray crystallography. Structure, 2, 271-282.
    • (1994) Structure , vol.2 , pp. 271-282
    • Cheng, R.H.1    Reddy, V.S.2    Olson, N.H.3    Fisher, A.J.4    Baker, T.S.5    Johnson, J.E.6
  • 5
    • 0028847173 scopus 로고
    • Proteolytic and conformational control of virus capsid maturation: The bacteriophage HK97 system
    • Conway, J. F., Duda, R. L., Cheng, N., Hendrix, R. W. & Steven, A. C. (1995). Proteolytic and conformational control of virus capsid maturation: the bacteriophage HK97 system. J. Mol. Biol. 253, 86-99.
    • (1995) J. Mol. Biol. , vol.253 , pp. 86-99
    • Conway, J.F.1    Duda, R.L.2    Cheng, N.3    Hendrix, R.W.4    Steven, A.C.5
  • 6
    • 0028130861 scopus 로고
    • Low-resolution real-space envelopes: The application of the condensing-protocol approach to the ab initio macromolecular phase problem of a variety of examples
    • David, P. R. & Subbiah, S. (1994). Low-resolution real-space envelopes: the application of the condensing-protocol approach to the ab initio macromolecular phase problem of a variety of examples. Acta Crystallog. sect. D, 50, 132-138.
    • (1994) Acta Crystallog. Sect. D , vol.50 , pp. 132-138
    • David, P.R.1    Subbiah, S.2
  • 8
    • 0028927348 scopus 로고
    • Genetic basis of bacteriophage HK97 prohead assembly
    • Duda, R. L., Martincic, K. & Hendrix, R. W. (1995b). Genetic basis of bacteriophage HK97 prohead assembly. J. Mol. Biol. 247, 636-647.
    • (1995) J. Mol. Biol. , vol.247 , pp. 636-647
    • Duda, R.L.1    Martincic, K.2    Hendrix, R.W.3
  • 9
    • 0001753477 scopus 로고
    • Structural studies of virus
    • (Maramorosch, K. & Koprowski, H., eds), Academic Press, New York
    • Finch, J. T. & Holmes, K. C. (1967). Structural studies of virus. In Methods in Virology III (Maramorosch, K. & Koprowski, H., eds), pp. 351-474, Academic Press, New York.
    • (1967) Methods in Virology III , pp. 351-474
    • Finch, J.T.1    Holmes, K.C.2
  • 11
    • 0027535332 scopus 로고
    • Crystallization of virus like particles assembled from flock house virus coat protein expressed in a baculovirus system
    • Fisher, A. J., Mckinney, A. R., Schneemann, A., Rueckert, R. R. & Johnson, J. E. (1993). Crystallization of virus like particles assembled from flock house virus coat protein expressed in a baculovirus system. J. Virol. 67, 2950-2953.
    • (1993) J. Virol. , vol.67 , pp. 2950-2953
    • Fisher, A.J.1    Mckinney, A.R.2    Schneemann, A.3    Rueckert, R.R.4    Johnson, J.E.5
  • 12
    • 0027518457 scopus 로고
    • Ordered duplex RNA controls capsid architecture in an icosahedral animal virus
    • Fisher, A. J. & Johnson, J. E. (1993). Ordered duplex RNA controls capsid architecture in an icosahedral animal virus. Nature, 361, 176-179.
    • (1993) Nature , vol.361 , pp. 176-179
    • Fisher, A.J.1    Johnson, J.E.2
  • 14
    • 0028797894 scopus 로고
    • Fast ab initio calculation of solvent envelopes for protein structures
    • Harris, G. (1995). Fast ab initio calculation of solvent envelopes for protein structures. Acta Crystallog. sect. D, 51, 695-702.
    • (1995) Acta Crystallog. Sect. D , vol.51 , pp. 695-702
    • Harris, G.1
  • 15
    • 0014693815 scopus 로고
    • Structure of tomato bushy stunt virus. I. Spherically averaged electron density
    • Harrison, S. C. (1969). Structure of tomato bushy stunt virus. I. Spherically averaged electron density. J. Mol. Biol. 42, 457-483.
    • (1969) J. Mol. Biol. , vol.42 , pp. 457-483
    • Harrison, S.C.1
  • 17
    • 0016709155 scopus 로고
    • On the interpretation of small-angle X-ray solution scattering from spherical viruses
    • Jack, A. & Harrison, S. C. (1975). On the interpretation of small-angle X-ray solution scattering from spherical viruses. J. Mol. Biol, 99, 15-25.
    • (1975) J. Mol. Biol , vol.99 , pp. 15-25
    • Jack, A.1    Harrison, S.C.2
  • 18
    • 84886625747 scopus 로고
    • The structure of Southern bean mosaic virus at 22. 5 Å resolution
    • Johnson, J. E., Akimoto, T., Suck, D., Rayment, I. & Rossmann, M. G. (1976). The structure of Southern bean mosaic virus at 22. 5 Å resolution. Virology, 75, 394-400.
    • (1976) Virology , vol.75 , pp. 394-400
    • Johnson, J.E.1    Akimoto, T.2    Suck, D.3    Rayment, I.4    Rossmann, M.G.5
  • 19
    • 0002552477 scopus 로고
    • A, yaap, asap, @#*? A set of averaging programs
    • (Dodson, E. J., Gover, S. & Wolf, W., eds), Daresbury Laboratory, Daresbury, England
    • Jones, T. A. (1992). A, yaap, asap, @#*? A set of averaging programs. In CCP4 Study Weekend, 1992: Molecular Replacement (Dodson, E. J., Gover, S. & Wolf, W., eds), pp. 91-105, Daresbury Laboratory, Daresbury, England.
    • (1992) CCP4 Study Weekend, 1992: Molecular Replacement , pp. 91-105
    • Jones, T.A.1
  • 20
    • 0002700643 scopus 로고
    • Halloween-masks and bones
    • (Bailey, S., Hubbard, R. & Waller, D., eds), Warrington, UK, SERC Daresbury Laboratory
    • Kleywegt, G. J. & Jones, T. A. (1994). Halloween-masks and bones. In From First Map to Final Model (Bailey, S., Hubbard, R. & Waller, D., eds), pp. 59-66, Warrington, UK, SERC Daresbury Laboratory.
    • (1994) From First Map to Final Model , pp. 59-66
    • Kleywegt, G.J.1    Jones, T.A.2
  • 21
    • 13144295242 scopus 로고    scopus 로고
    • Low resolution single crystal data collection for initial phase determination: Heat-shock protein hsc20
    • (Dunn, L., ed.), Stanford Synchrotron Radiation Laboratory, Stanford
    • Luecke, H., Tsuruta, H., Vickery, L. E. & Subbiah, S. (1997). Low resolution single crystal data collection for initial phase determination: heat-shock protein hsc20. In 1996 SSRL Activity Report (Dunn, L., ed.), pp. A-157, Stanford Synchrotron Radiation Laboratory, Stanford.
    • (1997) 1996 SSRL Activity Report
    • Luecke, H.1    Tsuruta, H.2    Vickery, L.E.3    Subbiah, S.4
  • 22
    • 0029175753 scopus 로고
    • On the ab initio solution of the phase problem for macromolecules at very low-resolution: The few atoms model method
    • Lunin, V. Y., Lunina, N. L., Petrova, T. E., Vernoslova, E. A., Urzhumtsev, A. G. & Podjarny, A. D. (1995). On the ab initio solution of the phase problem for macromolecules at very low-resolution: the few atoms model method. Acta Crystallog. sect. D, 51, 896-903.
    • (1995) Acta Crystallog. Sect. D , vol.51 , pp. 896-903
    • Lunin, V.Y.1    Lunina, N.L.2    Petrova, T.E.3    Vernoslova, E.A.4    Urzhumtsev, A.G.5    Podjarny, A.D.6
  • 23
  • 24
    • 0003299426 scopus 로고    scopus 로고
    • A genetic algorithm for the ab initio phasing of icosahedral viruses
    • Miller, S., Hogle, J. & Filman, D. (1996). A genetic algorithm for the ab initio phasing of icosahedral viruses. Acta Crystallog. sect. D, 52, 235-251.
    • (1996) Acta Crystallog. Sect. D , vol.52 , pp. 235-251
    • Miller, S.1    Hogle, J.2    Filman, D.3
  • 25
    • 0030576341 scopus 로고    scopus 로고
    • The 2.8 Å structure of a T = 4 animal virus and its implications for membrane translocation of RNA
    • Munshi, S., Liljas, L., Cavarelli, J., Bomu, W., McKinney, B., Reddy, V. & Johnson, J. (1996). The 2.8 Å structure of a T = 4 animal virus and its implications for membrane translocation of RNA. J. Mol. Biol. 261, 1-10.
    • (1996) J. Mol. Biol. , vol.261 , pp. 1-10
    • Munshi, S.1    Liljas, L.2    Cavarelli, J.3    Bomu, W.4    McKinney, B.5    Reddy, V.6    Johnson, J.7
  • 26
    • 0002452464 scopus 로고
    • Oscillation data reduction program
    • (Sawyer, L., Isaacs, N. & Bailey, S., eds), SERC Daresbury Laboratory, Warrington, UK
    • Otwinowski, Z. (1993). Oscillation data reduction program. In Proceedings of the CCP4 Study Weekend: Data Collection and Processing (Sawyer, L., Isaacs, N. & Bailey, S., eds), pp. 56-62, SERC Daresbury Laboratory, Warrington, UK.
    • (1993) Proceedings of the CCP4 Study Weekend: Data Collection and Processing , pp. 56-62
    • Otwinowski, Z.1
  • 27
    • 0001681837 scopus 로고
    • Molecular replacement method at low resolution: Optimum strategy and intrinsic limitations as determined by calculations on icosahedral virus models
    • Rayment, I. (1983). Molecular replacement method at low resolution: optimum strategy and intrinsic limitations as determined by calculations on icosahedral virus models. Acta Crystallog. sect. A, 39, 102-116.
    • (1983) Acta Crystallog. Sect. A , vol.39 , pp. 102-116
    • Rayment, I.1
  • 28
    • 0020031457 scopus 로고
    • Polyoma virus capsid structure at 22.5 Å resolution
    • Rayment, I., Baker, T. S., Caspar, D. L. D. & Murakami, W. T. (1982). Polyoma virus capsid structure at 22.5 Å resolution. Nature, 295, 110-115.
    • (1982) Nature , vol.295 , pp. 110-115
    • Rayment, I.1    Baker, T.S.2    Caspar, D.L.D.3    Murakami, W.T.4
  • 29
    • 0000731339 scopus 로고
    • Processing oscillation diffraction data for very large unit cells with an automatic convolution technique and profile fitting
    • Rossmann, M. G. (1979). Processing oscillation diffraction data for very large unit cells with an automatic convolution technique and profile fitting. J. Appl. Crystallog. 12, 225.
    • (1979) J. Appl. Crystallog. , vol.12 , pp. 225
    • Rossmann, M.G.1
  • 31
    • 0020523623 scopus 로고
    • The spherically averaged structures of cowpea mosaic virus components by X-ray solution scattering
    • Schmidt, T., Johnson, J. E. & Phillips, W. E. (1983). The spherically averaged structures of cowpea mosaic virus components by X-ray solution scattering. Virology, 127, 65-73.
    • (1983) Virology , vol.127 , pp. 65-73
    • Schmidt, T.1    Johnson, J.E.2    Phillips, W.E.3
  • 32
    • 0028318586 scopus 로고
    • Reconstitution of Flock House provirions: A model system for studying structure and assembly
    • Schneemann, A., Gallagher, T. M. & Rueckert, R. R. (1994). Reconstitution of Flock House provirions: a model system for studying structure and assembly. J. Virol. 68, 4547-4556.
    • (1994) J. Virol. , vol.68 , pp. 4547-4556
    • Schneemann, A.1    Gallagher, T.M.2    Rueckert, R.R.3
  • 33
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • SERC Daresbury Laboratory (1994). The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D, 50, 760-763.
    • (1994) Acta Crystallog. Sect. D , vol.50 , pp. 760-763
  • 34
    • 0025909189 scopus 로고
    • X-ray solution scattering of sindbis virus. Changes in conformation induced at low pH
    • Stubbs, M. J., Miller, A., Sizer, P. J. H., Stephenson, J. R. & Crooks, A. J. (1991). X-ray solution scattering of sindbis virus. Changes in conformation induced at low pH. J. Mol. Biol. 221, 39-42.
    • (1991) J. Mol. Biol. , vol.221 , pp. 39-42
    • Stubbs, M.J.1    Miller, A.2    Sizer, P.J.H.3    Stephenson, J.R.4    Crooks, A.J.5
  • 35
    • 0026416649 scopus 로고
    • Low-resolution real-space envelopes: An approach to the ab initio macromolecular phase problem
    • Subbiah, S. (1991). Low-resolution real-space envelopes: an approach to the ab initio macromolecular phase problem. Science, 252, 128-133.
    • (1991) Science , vol.252 , pp. 128-133
    • Subbiah, S.1
  • 36
    • 0028774704 scopus 로고
    • The three-dimensional distribution of RNA and protein in the interior of tomato bushy stunt virus: A neutron low-resolution single-crystal diffraction study
    • Timmins, P. A., Wild, D. & Witz, J. (1994). The three-dimensional distribution of RNA and protein in the interior of tomato bushy stunt virus: a neutron low-resolution single-crystal diffraction study. Structure, 2, 1191-1201.
    • (1994) Structure , vol.2 , pp. 1191-1201
    • Timmins, P.A.1    Wild, D.2    Witz, J.3
  • 38
    • 0029199267 scopus 로고
    • On the solution of the molecular-replacement problem at very low-resolution: Application to large complexes
    • Urzhumtsev, A. & Podjarny, A. (1995). On the solution of the molecular-replacement problem at very low-resolution: application to large complexes. Acta Crystallog. sect. D, 51, 888-895.
    • (1995) Acta Crystallog. Sect. D , vol.51 , pp. 888-895
    • Urzhumtsev, A.1    Podjarny, A.2
  • 39
    • 0032579807 scopus 로고    scopus 로고
    • Crystallization and preliminary X-ray analysis of the ds DNA bacteriophage HK97 mature empty capsid
    • Wikoff, W. R., Duda, R. L., Hendrix, R. W. & Johnson, J. E. (1998). Crystallization and preliminary X-ray analysis of the ds DNA bacteriophage HK97 mature empty capsid. Virology, 243, 113-118.
    • (1998) Virology , vol.243 , pp. 113-118
    • Wikoff, W.R.1    Duda, R.L.2    Hendrix, R.W.3    Johnson, J.E.4
  • 40
    • 0028791824 scopus 로고
    • Assembly in vitro of bacteriophage HK97 proheads
    • Xie, Z. & Hendrix, R. W. (1995). Assembly in vitro of bacteriophage HK97 proheads. J. Mol. Biol. 253, 74-85.
    • (1995) J. Mol. Biol. , vol.253 , pp. 74-85
    • Xie, Z.1    Hendrix, R.W.2
  • 41
    • 0029149195 scopus 로고
    • Determination of three-dimensional low-resolution viral structure from solution X-ray scattering data. Biophys
    • Zheng, Y., Doerschuk, P. C. & Johnson, J. E. (1995). Determination of three-dimensional low-resolution viral structure from solution X-ray scattering data. Biophys. J. 69, 619-639.
    • (1995) J. , vol.69 , pp. 619-639
    • Zheng, Y.1    Doerschuk, P.C.2    Johnson, J.E.3
  • 42
    • 13144261971 scopus 로고
    • Nucleic acids & nucleoproteins
    • (Glatter, O. & Kratky, O., eds), Academic Press, London
    • Zipper, P. (1982). Nucleic acids & nucleoproteins. In Small Angle X-ray Scattering (Glatter, O. & Kratky, O., eds), pp. 304-311, Academic Press, London.
    • (1982) Small Angle X-ray Scattering , pp. 304-311
    • Zipper, P.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.