Low-resolution density maps from atomic models: How stepping 'back' can be a step 'forward'

Journal of Structural Biology

Volumn 125, Issue 2-3, 1999, Pages 166-175

  Belnap, David M ^a   Kumar, Abhinav ^a   Folk, Jon T ^a   Smith, Thomas J ^a   Baker, Timothy S ^a  

^a PURDUE UNIVERSITY   (United States)

Author keywords

Correlation of cryoelectron microscopy and X ray crystallography; Cryoelectron microscopy; Modeling; Scanning transmission electron microscopy; Three dimensional image reconstruction; Truncation of resolution; X ray crystallography

Indexed keywords

ARTICLE; ATOMIC PARTICLE; CALIBRATION; COMPUTER PROGRAM; CRYOELECTRON MICROSCOPY; FOURIER TRANSFORMATION; IMAGE QUALITY; IMAGE RECONSTRUCTION; MACROMOLECULE; MOLECULAR MODEL; PHASE CONTRAST MICROSCOPE; PRIORITY JOURNAL; THREE DIMENSIONAL IMAGING; TRANSMISSION ELECTRON MICROSCOPY; X RAY CRYSTALLOGRAPHY;

EID: 0032809077     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1006/jsbi.1999.4093     Document Type: Article

References (51)

1. Bailey S. The CCP4 suite - Programs for protein crystallography. Acta Crystallogr. Sect. D. 50:1994;760-763.
2. Baker T. S., Drak J., Bina M. Reconstruction of the three-dimensional structure of simian virus 40 and visualization of the chromatin core. Proc. Natl. Acad. Sci. USA. 85:1988;422-426.
3. Baker T. S., Cheng R. H. A model-based approach for determining orientations of biological macromolecules imaged by cryo-electron microscopy. J. Struct. Biol. 116:1996;120-130.
4. Baker T. S., Johnson J. E. Low resolution meets high: Towards a resolution continuum from cells to atoms. Curr. Opin. Struct. Biol. 6:1996;585-594.
5. Belnap D. M., Grochulski W. D., Olson N. H., Baker T. S. Use of radial density plots to calibrate image magnification for frozen-hydrated specimens. Ultramicroscopy. 48:1993;347-358.
6. Belnap D. M., Olson N. H., Baker T. S. A method for establishing the handedness of biological macromolecules. J. Struct. Biol. 120:1997;44-51.
7. Beuron F., Maurizi M. R., Belnap D. M., Kocsis E., Booy F. P., Kessel M., Steven A. C. At sixes and sevens: Characterization of the symmetry mismatch of the ClpAP chaperone-assisted protease. J. Struct. Biol. 123:1998;248-259.
8. Böttcher B., Wynne S. A., Crowther R. A. Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature. 386:1997;88-91.
9. Brünger A. T., Kuriyan J., Karplus M. Crystallographic R factor refinement by molecular dynamics. Science. 235:1987;458-460.
10. Che Z., Olson N. H., Leippe D., Lee W.-M., Mosser A. G., Ruckert R. R., Baker T. S., Smith T. J. Antibody-mediated neutralization of human rhinovirus 14 explored by means of cryo-electron microscopy and X-ray crystallography of virus-Fab complexes. J. Virol. 72:1998;4610-4622.
11. Cheng R. H. Correlation of cryo-electron microscopic and X-ray data and compensation of the contrast transfer function. Proceedings of the 50th Annual Meeting of the Electron Microscopy Society of America. 1992;San Francisco Press, San Francisco. p. 996-997.
12. Cheng R. H., Reddy V. S., Olson N. H., Fisher A. J., Baker T. S., Johnson J. E. Functional implications of quasi-equivalence in a T = 3 icosahedral animal virus established by cryo-electron microscopy and X-ray crystallography. Structure. 2:1994;271-282.
13. Conway J. F., Cheng N., Zlotnick A., Wingfield P. T., Stahl S. J., Steven A. C. Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy. Nature. 386:1997;91-94.
14. Drenth J. Principles of Protein X-ray Crystallography. 1994;Springer-Verlag, New York.
15. Erickson H. P., Klug A. Measurement and compensation of defocusing and aberrations by Fourier processing of electron micrographs. Philos. Trans. R. Soc. London B. 261:1971;105-118.
16. Fisher A. J., Johnson J. E. Ordered duplex RNA controls capsid architecture in an icosahedral animal virus. Nature. 361:1993;176-179.
17. Furcinitti P. S., van Oostrum J., Burnett R. M. Adenovirus polypeptide IX revealed as capsid cement by difference images from electron microscopy and crystallography. EMBO J. 8:1989;3563-3570.
18. Griffith J. P., Griffith D. L., Rayment I., Murakami W. T., Caspar D. L. D. Inside polyomavirus at 25-Å resolution. Nature. 355:1992;652-654.
19. Grimes J. M., Jakana J., Ghosh M., Basak A. K., Roy P., Chiu W., Stuart D. I., Prasad B. V. V. An atomic model of the outer layer of the bluetongue virus core derived from X-ray crystallography and electron cryomicroscopy. Structure. 5:1997;885-893.
20. Grimes J. M., Burroughs J. N., Gouet P., Diprose J. M., Malby R., Ziéntara S., Mertens P. P. C., Stuart D. I. The atomic structure of the bluetongue virus core. Nature. 395:1998;470-478.
21. Hadfield A. T., Lee W.-M., Zhao R., Oliveira M. A., Minor I., Rueckert R. R., Rossmann M. G. The refined structure of human rhinovirus 16 at 2.15 Å resolution: Implications for the viral life cycle. Structure. 5:1997;427-441.
22. Henderson R., Baldwin J. M., Ceska T. A., Zemlin F., Beckmann E., Downing K. H. Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J. Mol. Biol. 213:1990;899-929.
23. Ilag L. L., Olson N. H., Dokland T., Music C. L., Cheng R. H., Bowen Z., McKenna R., Rossmann M. G., Baker T. S., Incardona N. L. DNA packaging intermediates of bacteriophage ΦX174. Structure. 3:1995;353-363.
24. Johnson J. E., Munshi S., Liljas L., Agrawal D., Olson N. H., Reddy V., Fisher A., McKinney B., Schmidt T., Baker T. S. Comparative studies of T = 3 and T = 4 icosahedral RNA insect viruses. Arch. Virol. 9:1994;497-512.
25. 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. Sect. A. 47:1991;110-119.
26. Kessel M., Maurizi M. R., Kim B., Kocsis E., Trus B. L., Singh S. K., Steven A. C. Homology in structural organization betweenE. coli. J. Mol. Biol. 250:1995;587-594.
27. Kühlbrandt W., Wang D. N., Fujiyoshi Y. Atomic model of plant light-harvesting complex by electron crystallography. Nature. 367:1994;614-621.
28. Kraulis P. J. Molscript - A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:1991;946-950.
29. Kumar A., Reddy V. S., Yusibov V., Chipman P. R., Hata Y., Fita I., Fukuyama K., Rossman M. G., Loesch-Fries L. S., Baker T. S., Johnson J. E. The structure of alfalfa mosaic virus capsid protein assembled as a T = 1 icosahedral particle at 4.0-Å resolution. J. Virol. 71:1997;7911-7916.
30. McKenna R., Xia D., Willingmann P., Ilag L. L., Krishnaswamy S., Rossmann M. G., Olson N. H., Baker T. S., Incardona N. L. Atomic structure of single-stranded DNA bacteriophage ΦX174 and its functional implications. Nature. 355:1992;137-143.
31. Merritt E. A., Bacon D. J. Raster3D: Photorealistic molecular graphics. Methods Enzymol. 277:1997;505-524.
32. Misell D. L. Image analysis, enhancement, and interpretation. Glauert A. M. Practical Methods in Electron Microscopy. 1978;Elsevier/North-Holland.
33. Munshi S., Liljas L., Cavarelli J., Bomu W., McKinney B., Reddy V., Johnson J. E. The 2.8 angstrom structure of a T = 4 animal virus and its implications for membrane translocation of RNA. J. Mol. Biol. 261:1996;1-10.
34. Nogales E., Wolf S. G., Downing K. H. Structure of the αβ tubulin dimer by electron crystallography. Nature. 391:1998;199-203.
35. Olson N. H., Baker T. S., Willingmann P., Incardona N. L. The three-dimensional structure of frozen-hydrated bacteriophage ΦX174. J. Struct. Biol. 108:1992;168-175.
36. Rossmann M. G., Arnold E., Erickson J. W., Frankenberger E. A., Griffith J. P., Hecht H. J., Johnson J. E., Kamer G., Luo M., Mosser A. G., Rueckert R. R., Sherry B., Vriend G. Structure of a human common cold virus and functional relationship to other picornaviruses. Nature. 317:1985;145-153.
37. Smith T. J., Olson N. H., Cheng R. H., Liu H., Chase E. S., Lee W. M., Leippe D. M., Mosser A. G., Rueckert R. R., Baker T. S. Structure of human rhinovirus complexed with Fab fragments from a neutralizing antibody. J. Virol. 67:1993;1148-1158.
38. Smith T. J., Chase E. S., Schmidt T. J., Olson N. H., Baker T. S. Neutralizing antibody to human rhinovirus 14 penetrates the receptor-binding canyon. Nature. 383:1996;350-354.
39. Speir J. A., Munshi S., Wang G., Baker T. S., Johnson J. E. Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryo-electron microscopy. Structure. 3:1995;63-78.
40. Stauffacher C. V., Usha R., Harrington M., Schmidt T., Hosur M. V., Johnson J. E. The structure of cowpea mosaic virus at 3.5 Å resolution. Morjas D., Drenth J., Strandberg B., Suck D., Wilson K. Crystallography in Molecular Biology. 1987;293-308 Plenum, New York.
41. Stehle T., Harrison S. C. Crystal structures of murine polyomavirus in complex with straight-chain and branched-chain sialyloligosaccharide receptor fragments. Structure. 4:1996;183-194.
42. Stehle T., Gamblin S. J., Yan Y., Harrison S. C. The structure of simian virus 40 refined at 3.1 Å resolution. Structure. 4:1996;165-182.
43. Stewart P. L., Burnett R. M., Cyrklaff M., Fuller S. D. Image reconstruction reveals the complex molecular organization of adenovirus. Cell. 67:1991;145-154.
44. Stewart P. L., Fuller S. D., Burnett R. M. Difference imaging of adenovirus: Bridging the resolution gap between X-ray crystallography and electron microscopy. EMBO J. 12:1993;2589-2599.
45. Trus B. L., Roden R. B. S., Greenstone H. L., Vrhel M., Schiller J. T., Booy F. P. Novel structural features of bovine papillomavirus capsid revealed by a three-dimensional reconstruction to 9 Å resolution. Nature Struct. Biol. 4:1997;413-420.
46. Volkmann N., Hanein D. Quantitative fitting of atomic models into observed densities derived by electron microscopy. J. Struct. Biol. 125:1999;176-184.
47. Wang G., Porta C., Chen Z., Baker T. S., Johnson J. E. Identification of a Fab interaction footprint site on an icosahedral virus by cryoelectron microscopy and X-ray crystallography. Nature. 355:1992;275-278.
48. Wikoff W. R., Wang G., Parrish C. R., Cheng R. H., Strassheim M. L., Baker T. S., Rossmann M. G. The structure of a neutralized virus: Canine parvovirus complexed with neutralizing antibody fragment. Structure. 2:1994;595-607.
49. Wriggers W., Milligan R. A., Schulten K., McCammon J. A. Self-organizing neural networks bridge the biomolecular resolution gap. J. Mol. Biol. 284:1998;1247-1254.
50. Wriggers W., Milligan R. A., McCammon J. A. Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. J. Struct. Biol. 125:1999;185-195.
51. Zhang X.-J., Matthews B. W. EDPDB: A multi-functional tool for protein structure analysis. J. Appl. Crystallogr. 28:1995;624-630.