Low-resolution structure refinement in electron microscopy

Journal of Structural Biology

Volumn 144, Issue 1-2, 2003, Pages 144-151

  Chen, James Z ^a   Fürst, Johannes ^a,b   Chapman, Michael S ^c   Grigorieff, Nikolaus ^a  

^a BRANDEIS UNIVERSITY   (United States)

^b UNIVERSITY OF INNSBRUCK   (Austria)

^c FLORIDA STATE UNIVERSITY   (United States)

Author keywords

Electron density map; Electron microscopy; Empirical force field; Macromolecular structure; Real space structure refinement

Indexed keywords

ACTIN; ADENOSINE TRIPHOSPHATASE; AMINO ACID;

ARTICLE; CONFORMATIONAL TRANSITION; ELECTRON MICROSCOPY; IMAGE RECONSTRUCTION; OPTICAL RESOLUTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN STRUCTURE; SIGNAL NOISE RATIO; SIMULATION; STEREOCHEMISTRY; X RAY CRYSTALLOGRAPHY;

EID: 0344120716     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jsb.2003.09.008     Document Type: Article

References (41)

1. Bottcher B., Wayne S.A., Crowther R.A. Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature. 385:1997;26-27.
2. Brünger A.T. X-PLOR Version 3.1: A System for X-ray Crystallography and NMR. 1992;Yale University Press, New Haven.
3. Brünger A.T. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature. 355:1992;472-475.
4. Brünger A.T., Kuriyan J., Karplus M. Crystallographic R factor refinement by molecular dynamics. Science. 235:1987;458-460.
5. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S., Reed R.J., Rice L.M., Simonson T., Warren G.L. Cyrstallography & NMR system: a new software suite for macromolecular strcuture determination. Acta Crystallogr. D. 54:1998;905-921.
6. Chapman M.S. Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron-density function. Acta Crystallogr. A. 51:1995;69-80.
7. Chen J.Z., Chapman M.S. Conformational disorder of proteins assessed by real space molecular dynamics refinement. Biophys. J. 80:2001;1466-1472.
8. Chen J.Z., Blanc E., Chapman M.S. Real space molecular dynamics structural refinement. Acta Crystallogr. D. 55:1999;464-468.
9. Chen J.Z., Blanc E., Chapman M.S. Improved free R-factors for the cross validation of macromolecular structures. Acta Crystallogr. D. 55:1999;219-224.
10. Chen L.F., Blanc E., Chapman M.S., Taylor K.A. Real space refinement of acto-myosin structures from sectioned muscle. J. Struct. Biol. 133:2001;221-232.
11. Chiu W., Rixon F.J. High resolution structural studies of complex icosahedral viruses: a brief overview. Virus Res. 82:2002;9-17.
12. Egelman, E., DeRosier, D., 2003. Personal communication.
13. Frank J., Agrawal R.K. A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature. 406:2000;318-322.
14. Frank, B.S., Vardar, D., Chishti, A.H., McKnight, C.J., 2003. The NMR structure dematin headpiece reveals a dynamic loop that is conformationally altered upon phosphorylation at a distal site, personal communication.
15. Frank J., Radermacher M., Penczek P., Zhu J., Li Y., Ladjadj M., Leith A. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116:1996;190-199.
16. Fürst J., Sutton R.B., Chen J.Z., Brünger A.T., Grigorieff N. Electron cryo-microscopy structure of. N -ethyl maleimide sensitive factor at 11 Å resolution EMBO J. 22:2003;4365-4374.
17. Gao H., Sengupta J., Valle M., Korostelev A., Eswar N., Stagg S.M., Roey P.V., Agrawal R.K., Harvey S.C., Sali A., Chapman M.S., Frank J. Study of the structural dynamics of the E. Coli 70S ribosome using real-space refinement. Cell. 113:2003;789-801.
18. Golas M.M., Sander B., Will C.L., Luhrmann R., Stark H. Molecular architecture of the multiprotein splicing factor SF31. Science. 300:2003;980-984.
19. Grigorieff N. Resolution measurement in structures derived from single particles. Acta Crystallogr. D. 56:2000;1270-1277.
20. Grigorieff N., Ceska T.A., Downing K.H., Baldwin J.M., Henderson R. Electron-crystallographic refinement of the structure of bacteriorhodopsin. JMB. 259:1996;393-421.
21. Hanson P.I., Roth R., Morisaki H., Jahn R., Heuser J.E. Structure and conformational changes in NSF and its membrane receptor complexes visualized by quick-freeze/deep-etch electron microscopy. Cell. 90:1997;523-535.
22. Harauz G., van Heel M. Exact filters for general geometry three-dimensional reconstruction. Optik. 73:1986;146-156.
23. Henderson R., Baldwin J.M., Ceska T.A., Zemlin F., Beckmann E., Downing K.H. An atomic model for the structure of bacteriorhodopsin. Biochem. Soc. Trans. 18:1990;844.
24. Huang C.C., Couch G.S., Pettersen E.F., Ferrin T.E. Chimera: an extensible molecular modeling application constructed using standard components. Pac. Symp. Biocomput. 1:1996;724.
25. Janin J., Henrick K., Moult J., Eyck L.T., Sternberg M.J.E., Vajda S., Vakser I., Wodak S.J. CAPRI: a critical assessment of predicted interactions. Proteins: Struct. Funct. Genet. 52:2003;2-9.
26. Jiang W., Baker M.L., Ludtke S.J., Chiu W. Bridging the information gap: computational tools for intermediate resolution structure interpretation. J. Mol. Biol. 308:2001;1033-1044.
27. Kabsch W., Mannherz H.G., Suck D., Pai E.F., Holmes K.C. Atomic structure of the Actin:DNAse I complex. Nature. 347:1990;37-44.
28. Korostelev A., Bertram R., Chapman M.S. Simulated annealing real-space refinement as a tool in model building. Acta Crystallogr. D. 58:2002;761-767.
29. Lenzen C.U., Steinmann D., Whiteheart S.W., Weis W.I. Crystal structure of the hexamerization domain of. N -ethylmaleimide-sensitive fusion protein Cell. 94:1998;525-536.
30. Miyazawa A., Fujiyoshi Y., Stowell M., Unwin N. Nicotinic acetylcholine receptor at 4.6. Å resolution: transverse tunnels in the channel wall J. Mol. Biol. 288:1999;765-786.
31. Morgan D.G., Macnab R.M., Francis N.R., DeRosier D.J. Domain organization of the subunit of the Salmonella typhimurium flagellar hook. J. Mol. Biol. 229:1993;79-84.
32. Rosenfeld A. Multiresolution Image Processing and Analysis. 1984;Springer, Berlin.
33. Roseman A.M. Docking structures of domains into maps from cryo-electron microscopy using local correlation. Acta Crystallogr. D. 56:2000;1332-1340.
34. Rossmann M.G., Bernal R., Pletnev S.V. Combining electron microscopic with X-ray crystallographic structures. J. Struct. Biol. 136:2001;190-200.
35. Samatey, F.A., Matsunami, H., Imada, K., Nagashima, S., Namba, K., 2003. Personal communication.
36. Saxton W.O., Baumeisterm W. The correlation averaging of a regularly arranged bacterial cell envelop protein. J. Microsc. 127:1982;127-138.
37. Shaikh, T.R., Thomas, D., Francis, N.R., DeRosier, D.J., 2003a. Personal communication.
38. Shaikh T.R., Hegerl R., Frank J. An approach to examining model dependence in em reconstructions using cross-validation. J. Struct. Biol. 142:2003;30-310.
39. Volkmann N., Hanein D. Quantitative fitting of atomic models into observed densities by electron microscopy. J. Struct. Biol. 125:1999;176-184.
40. 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.
41. Yu R.C., Hanson P.I., Jahn R., Brünger A.T. Structure of the ATP-dependent oligomerization domain of. N -ethylmaleimide sensitive factor complexed with ATP Nat. Struct. Biol. 5:1998;803-811.