Subtomogram analysis using the Volta phase plate

Journal of Structural Biology

Volumn 197, Issue 2, 2017, Pages 94-101

  Khoshouei, Maryam ^a   Pfeffer, Stefan ^a   Baumeister, Wolfgang ^a   Förster, Friedrich ^a,b   Danev, Radostin ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^b UTRECHT UNIVERSITY   (Netherlands)

Author keywords

Cryo electron tomography; Ribosome; Subtomogram analysis; Volta phase plate

Indexed keywords

80S RIBOSOME RNA; RIBOSOME RNA; UNCLASSIFIED DRUG;

ACCURACY; ANALYTICAL EQUIPMENT; ARTICLE; CONTRAST TRANSMISSION ELECTRON MICROSCOPY; CONTROLLED STUDY; ELECTRON TOMOGRAPHY; INTERMETHOD COMPARISON; OSCILLATION; SIGNAL NOISE RATIO; STRUCTURE ANALYSIS; SUBTOMOGRAM ANALYSIS; TRANSMISSION ELECTRON MICROSCOPY; VOLTA PHASE PLATE; ANIMAL; CRYOELECTRON MICROSCOPY; DEVICES; HUMAN; PROCEDURES; RIBOSOME; ULTRASTRUCTURE;

ANIMALS; CRYOELECTRON MICROSCOPY; ELECTRON MICROSCOPE TOMOGRAPHY; HUMANS; MICROSCOPY, ELECTRON, TRANSMISSION; RIBOSOMES; SIGNAL-TO-NOISE RATIO;

EID: 84973538552     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2016.05.009     Document Type: Article

References (34)

1. Anger, A.M., Armache, J.P., Berninghausen, O., Habeck, M., Subklewe, M., Wilson, D.N., Beckmann, R., Structures of the human and Drosophila 80S ribosome. Nature 497 (2013), 80–85.
2. Asano, S., Fukuda, Y., Beck, F., Aufderheide, A., Forster, F., Danev, R., Baumeister, W., Proteasomes. A molecular census of 26S proteasomes in intact neurons. Science 347 (2015), 439–442.
3. Behrmann, E., Loerke, J., Budkevich, T.V., Yamamoto, K., Schmidt, A., Penczek, P.A., Vos, M.R., Burger, J., Mielke, T., Scheerer, P., Spahn, C.M., Structural snapshots of actively translating human ribosomes. Cell 161 (2015), 845–857.
4. Ben-Shem, A., Jenner, L., Yusupova, G., Yusupov, M., Crystal structure of the eukaryotic ribosome. Science 330 (2010), 1203–1209.
5. Ben-Shem, A., Garreau de Loubresse, N., Melnikov, S., Jenner, L., Yusupova, G., Yusupov, M., The structure of the eukaryotic ribosome at 3.0 A resolution. Science 334 (2011), 1524–1529.
6. Brandt, F., Etchells, S.A., Ortiz, J.O., Elcock, A.H., Hartl, F.U., Baumeister, W., The native 3D organization of bacterial polysomes. Cell 136 (2009), 261–271.
7. Briggs, J.A., Structural biology in situ–the potential of subtomogram averaging. Curr. Opin. Struct. Biol. 23 (2013), 261–267.
8. Danev, R., Baumeister, W., Cryo-EM single particle analysis with the Volta phase plate. Elife, 2016, 5.
9. Danev, R., Buijsse, B., Khoshouei, M., Plitzko, J.M., Baumeister, W., Volta potential phase plate for in-focus phase contrast transmission electron microscopy. Proc. Natl. Acad. Sci. U.S.A. 111 (2014), 15635–15640.
10. Eibauer, M., Hoffmann, C., Plitzko, J.M., Baumeister, W., Nickell, S., Engelhardt, H., Unraveling the structure of membrane proteins in situ by transfer function corrected cryo-electron tomography. J. Struct. Biol. 180 (2012), 488–496.
11. Fernandez, J.J., Li, S., Crowther, R.A., CTF determination and correction in electron cryotomography. Ultramicroscopy 106 (2006), 587–596.
12. Forster, F., Hegerl, R., Structure determination in situ by averaging of tomograms. Methods Cell Biol. 79 (2007), 741–767.
13. Forster, F., Han, B.G., Beck, M., Visual proteomics. Methods Enzymol. 483 (2010), 215–243.
14. Frangakis, A.S., Bohm, J., Forster, F., Nickell, S., Nicastro, D., Typke, D., Hegerl, R., Baumeister, W., Identification of macromolecular complexes in cryoelectron tomograms of phantom cells. Proc. Natl. Acad. Sci. U.S.A. 99 (2002), 14153–14158.
15. Fukuda, Y., Laugks, U., Lucic, V., Baumeister, W., Danev, R., Electron cryotomography of vitrified cells with a Volta phase plate. J. Struct. Biol. 190 (2015), 143–154.
16. Hrabe, T., Chen, Y., Pfeffer, S., Cuellar, L.K., Mangold, A.V., Forster, F., PyTom: a python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis. J. Struct. Biol. 178 (2012), 177–188.
17. Jenner, L., Melnikov, S., Garreau de Loubresse, N., Ben-Shem, A., Iskakova, M., Urzhumtsev, A., Meskauskas, A., Dinman, J., Yusupova, G., Yusupov, M., Crystal structure of the 80S yeast ribosome. Curr. Opin. Struct. Biol. 22 (2012), 759–767.
18. Khoshouei, M., Radjainia, M., Phillips, A.J., Gerrard, J.A., Mitra, A.K., Plitzko, J.M., Baumeister, W., Danev, R., Volta phase plate cryo-EM of the small protein complex Prx3. Nat. Commun., 7, 2016, 10534.
19. Koster, A.J., Van den Bos, A., Van der Mast, K.D., An autofocus method for a TEM. Ultramicroscopy 21 (1987), 209–222.
20. Li, X., Mooney, P., Zheng, S., Booth, C.R., Braunfeld, M.B., Gubbens, S., Agard, D.A., Cheng, Y., Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat. Methods 10 (2013), 584–590.
21. Lucic, V., Rigort, A., Baumeister, W., Cryo-electron tomography: the challenge of doing structural biology in situ. J. Cell Biol. 202 (2013), 407–419.
22. Mahamid, J., Pfeffer, S., Schaffer, M., Villa, E., Danev, R., Kuhn-Cuellar, L., Förster, F., Hyman, A., Plitzko, J., Baumeister, W., Visualizing the molecular sociology at the HeLa cell nuclear periphery. Science 351 (2016), 969–972.
23. Mastronarde, D.N., Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152 (2005), 36–51.
24. Melnikov, S., Ben-Shem, A., Garreau de Loubresse, N., Jenner, L., Yusupova, G., Yusupov, M., One core, two shells: bacterial and eukaryotic ribosomes. Nat. Struct. Mol. Biol. 19 (2012), 560–567.
25. Myasnikov, A.G., Afonina, Z.A., Menetret, J.F., Shirokov, V.A., Spirin, A.S., Klaholz, B.P., The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes. Nat. Commun., 5, 2014, 5294.
26. Pfeffer, S., Brandt, F., Hrabe, T., Lang, S., Eibauer, M., Zimmermann, R., Forster, F., Structure and 3D arrangement of endoplasmic reticulum membrane-associated ribosomes. Structure 20 (2012), 1508–1518.
27. Pfeffer, S., Dudek, J., Gogala, M., Schorr, S., Linxweiler, J., Lang, S., Becker, T., Beckmann, R., Zimmermann, R., Forster, F., Structure of the mammalian oligosaccharyl-transferase complex in the native ER protein translocon. Nat. Commun., 5, 2014, 3072.
28. Pfeffer, S., Woellhaf, M.W., Herrmann, J.M., Forster, F., Organization of the mitochondrial translation machinery studied in situ by cryoelectron tomography. Nat. Commun., 6, 2015, 6019.
29. Scheres, S.H., Chen, S., Prevention of overfitting in cryo-EM structure determination. Nat. Methods 9 (2012), 853–854.
30. Schuwirth, B.S., Borovinskaya, M.A., Hau, C.W., Zhang, W., Vila-Sanjurjo, A., Holton, J.M., Cate, J.H., Structures of the bacterial ribosome at 3.5 A resolution. Science 310 (2005), 827–834.
31. Selmer, M., Dunham, C.M., Murphy, F.V.T., Weixlbaumer, A., Petry, S., Kelley, A.C., Weir, J.R., Ramakrishnan, V., Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313 (2006), 1935–1942.
32. Steitz, T.A., A structural understanding of the dynamic ribosome machine. Nat. Rev. Mol. Cell Biol. 9 (2008), 242–253.
33. Voorhees, R.M., Fernandez, I.S., Scheres, S.H., Hegde, R.S., Structure of the mammalian ribosome-Sec61 complex to 3.4 A resolution. Cell 157 (2014), 1632–1643.
34. Yusupov, M.M., Yusupova, G.Z., Baucom, A., Lieberman, K., Earnest, T.N., Cate, J.H., Noller, H.F., Crystal structure of the ribosome at 5.5 A resolution. Science 292 (2001), 883–896.