On the interpretation of electron microscopic maps of biological macromolecules

Protein Science

Volumn 26, Issue 1, 2017, Pages 122-129

  Wang, Jimin ^a   Moore, Peter B ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

electric potential; electron atomic scattering factor; electron density; electron microscopy; electron scattering; X ray scattering

Indexed keywords

BETA GALACTOSIDASE; CARBOXYLIC ACID; NUCLEIC ACID; NUCLEIC ACID BASE; PHOSPHATE; RNA;

ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; DENSITY; ELECTRIC POTENTIAL; ELECTRON; ELECTRON MICROSCOPY; MACROMOLECULE; PRIORITY JOURNAL; RADIATION SCATTERING; RIBOSOME; RNA SEQUENCE; CRYOELECTRON MICROSCOPY; PROCEDURES; THREE DIMENSIONAL IMAGING; ULTRASTRUCTURE;

BETA-GALACTOSIDASE; CRYOELECTRON MICROSCOPY; IMAGING, THREE-DIMENSIONAL; RIBOSOMES; RNA;

EID: 84991585689     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.3060     Document Type: Article

References (31)

1. Henderson R (2015) Overview and future of single particle electron cryomicroscopy. Arch Biochem Biophys 581:19–24.
2. Subramaniam S, Kuhlbrandt W, Henderson R (2016) CryoEM at IUCrJ: a new era. IUCr J 3:3–7.
3. Subramaniam S, Earl LA, Falconieri V, Milne JL, Egelman EH (2016) Resolution advances in cryo-EM enable application to drug discovery. Curr Opin Struct Biol 41:194–202.
4. Shalev-Benami M, Zhang Y, Matzov D, Halfon Y, Zackay A, Rozenberg H, Zimmerman E, Bashan A, Jaffe CL, Yonath A, Skiniotis G (2016) 2.8-A cryo-EM structure of the large ribosomal subunit from the eukaryotic parasite Leishmania. Cell Rep 16:288–294.
5. Fischer N, Neumann P, Konevega AL, Bock LV, Ficner R, Rodnina MV, Stark H (2015) Structure of the E. coli ribosome-EF-Tu complex at <3 A resolution by Cs-corrected cryo-EM. Nature 520:567–570.
6. Bartesaghi A, Merk A, Banerjee S, Matthies D, Wu X, Milne JL, Subramaniam S (2015) 2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitor. Science 348:1147–1151.
7. Merk A, Bartesaghi A, Banerjee S, Falconieri V, Rao P, Davis MI, Pragani R, Boxer MB, Earl LA, Milne JL, Subramaniam S (2016) Breaking cryo-EM resolution barriers to facilitate drug discovery. Cell 165:1698–1707.
8. Nogales E (2016) The development of cryo-EM into a mainstream structural biology technique. Nat Meth 13:24–27.
9. Glaeser RM (2016) How good can cryo-EM become? Nat Meth 13:28–32.
10. Mott NF (1930) The scattering of electrons by atoms. Proc Royal Soc Lond A127:658–665.
11. James RW (1930) X-ray crystallography, the fifth edition, Methuen's Monographs on Physical Subjects. Bell & Son's, London.
12. Chang S, Head-Gordon T, Glaeser RM, Downing KH (1999) Chemical bonding effects in the determination of protein structures by electron crystallography. Acta Cryst A55:305–313.
13. Koritsanszky T, Flaig R, Zobel D, Krane H, Morgenroth W, Luger P (1998) Accurate experimental electronic properties of dl-proline monohydrate obtained within 1 day. Science 279:356–358.
14. Yonekura K, Kato K, Ogasawara M, Tomita M, Toyoshima C (2015) Electron crystallography of ultrathin 3D protein crystals: atomic model with charges. Proc Natl Acad Sci USA 112:3368–3373.
15. Moore P (2012) Visualizing the invisible: imaging techniques for the structural biologist. Oxford; New York: Oxford University Press.
16. Kimura Y, Vassylyev DG, Miyazawa A, Kidera A, Matsushima M, Mitsuoka K, Murata K, Hirai T, Fujiyoshi Y (1997) Surface of bacteriorhodopsin revealed by high-resolution electron crystallography. Nature 389:206–211.
17. Mitsuoka K, Hirai T, Murata K, Miyazawa A, Kidera A, Kimura Y, Fujiyoshi Y (1999) The structure of bacteriorhodopsin at 3.0 A resolution based on electron crystallography: implication of the charge distribution. J Mol Biol 286:861–882.
18. Gonen T, Cheng Y, Sliz P, Hiroaki Y, Fujiyoshi Y, Harrison SC, Walz T (2005) Lipid-protein interactions in double-layered two-dimensional AQP0 crystals. Nature 438:633–638.
19. Gonen T, Sliz P, Kistler J, Cheng Y, Walz T (2004) Aquaporin-0 membrane junctions reveal the structure of a closed water pore. Nature 429:193–197.
20. Dunkle JA, Wang L, Feldman MB, Pulk A, Chen VB, Kapral GJ, Noeske J, Richardson JS, Blanchard SC, Cate JH (2011) Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Science 332:981–984.
21. Srinivasan AR, Sauers RR, Fenley MO, Boschitsch AH, Matsumoto A, Colasanti AV, Olson WK (2009) Properties of the nucleic-acid bases in free and Watson-Crick hydrogen-bonded states: Computational insights into the sequence-dependent features of double-helical DNA. Biophys Rev 1:13–20.
22. Prince E (2004) International Tables for Crystallography. Volume C., London, U.K.: Kluwer Academic Publishers.
23. Peng LM (1999) Electron atomic scattering factors and scattering potentials of crystals. Micron 30:625–648.
24. Grigorieff N, Ceska TA, Downing KH, Baldwin JM, Henderson R (1996) Electron-crystallographic refinement of the structure of bacteriorhodopsin. J Mol Biol 259:393–421.
25. Kuhlbrandt W, Wang DN, Fujiyoshi Y (1994) Atomic model of plant light-harvesting complex by electron crystallography. Nature 367:614–621.
26. Ravelli RB, McSweeney SM (2000) The 'fingerprint' that X-rays can leave on structures. Structure 8:315–328.
27. Weik M, Ravelli RB, Kryger G, McSweeney S, Raves ML, Harel M, Gros P, Silman I, Kroon J, Sussman JL (2000) Specific chemical and structural damage to proteins produced by synchrotron radiation. Proc Natl Acad Sci USA 97:623–628.
28. Hayward SB, Glaeser RM (1979) Radiation damage of purple membrane at low temperature. Ultramicroscopy 04:201–210.
29. Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS (2011) Overview of the CCP4 suite and current developments. Acta Cryst D67:235–242.
30. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Cryst D60:2126–2132.
31. DeLano WL (2002) The PyMOL Molecular Graphics System. http://www.pymol.org/.