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007
23. T.A. Steitz, A structural understanding of the dynamic ribosome machine. Nat. Rev. Mol. Cell
Biol. 9(3), 242–253 (2008). doi:10.1038/nrm2352
24. F. Brandt, L.A. Carlson, F.U. Hartl, W. Baumeister, K. Grunewald, The three-dimensional
organization of polyribosomes in intact human cells. Mol. Cell 39(4), 560–569 (2010). doi:10.
1016/j.molcel.2010.08.003
25. F. Brandt, S.A. Etchells, J.O. Ortiz, A.H. Elcock, F.U. Hartl, W. Baumeister, The native 3D
organization of bacterial polysomes. Cell 136(2), 261–271 (2009). doi:10.1016/j.cell.2008.11.
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26. A.G. Myasnikov, Z.A. Afonina, J.F. Menetret, V.A. Shirokov, A.S. Spirin, B.P. Klaholz, The
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Nat. Commun. 5, 5294 (2014). doi:10.1038/ncomms6294
27. Z.A. Afonina, A.G. Myasnikov, V.A. Shirokov, B.P. Klaholz, A.S. Spirin, Formation of
circular polyribosomes on eukaryotic mRNA without cap-structure and poly(A)-tail: a cryo
electron tomography study. Nucleic Acids Res. 42(14), 9461–9469 (2014). doi:10.1093/nar/
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28. Z.A. Afonina, A.G. Myasnikov, V.A. Shirokov, B.P. Klaholz, A.S. Spirin, Conformation
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(1), 618–628 (2015). doi:10.1093/nar/gku1270
29. J.O. Ortiz, F. Brandt, V.R. Matias, L. Sennels, J. Rappsilber, S.H. Scheres, M. Eibauer, F.U.
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30. S. Pfeffer, F. Brandt, T. Hrabe, S. Lang, M. Eibauer, R. Zimmermann, F. Forster, Structure
and 3D arrangement of endoplasmic reticulum membrane-associated ribosomes. Structure 20
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31. S. Pfeffer, J. Dudek, M. Gogala, S. Schorr, J. Linxweiler, S. Lang, T. Becker, R. Beckmann,
R. Zimmermann, F. Forster, Structure of the mammalian oligosaccharyl-transferase complex
in the native ER protein translocon. Nat. Commun. 5, 3072 (2014). doi:10.1038/ncomms4072
32. S. Pfeffer, L. Burbaum, P. Unverdorben, M. Pech, Y. Chen, R. Zimmermann, R. Beckmann,
F. Forster, Structure of the native Sec61 protein-conducting channel. Nat. Commun. 6, 8403
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33. S. Pfeffer, M.W. Woellhaf, J.M. Herrmann, F. Forster, Organization of the mitochondrial
translation machinery studied in situ by cryoelectron tomography. Nat. Commun. 6, 6019
(2015). doi:10.1038/ncomms7019
34. P. Unverdorben, F. Beck, P. Sledz, A. Schweitzer, G. Pfeifer, J.M. Plitzko, W. Baumeister,
F. Forster, Deep classification of a large cryo-EM dataset defines the conformational
landscape of the 26S proteasome. Proc. Natl. Acad. Sci. U.S.A. 111(15), 5544–5549 (2014).
doi:10.1073/pnas.1403409111
35. T. Movassagh, K.H. Bui, H. Sakakibara, K. Oiwa, T. Ishikawa, Nucleotide-induced global
conformational changes of flagellar dynein arms revealed by in situ analysis. Nat. Struct. Mol.
Biol. 17(6), 761–767 (2010). doi:10.1038/nsmb.1832
36. J. Lin, K. Okada, M. Raytchev, M.C. Smith, D. Nicastro, Structural mechanism of the dynein
power stroke. Nat. Cell Biol. 16(5), 479–485 (2014). doi:10.1038/ncb2939
37. G. Pigino, K.H. Bui, A. Maheshwari, P. Lupetti, D. Diener, T. Ishikawa, Cryoelectron
tomography of radial spokes in cilia and flagella. J. Cell Biol. 195(4), 673–687 (2011). doi:10.
1083/jcb.201106125
38. T. Oda, H. Yanagisawa, M. Kikkawa, Detailed structural and biochemical characterization of
the nexin-dynein regulatory complex. Mol. Biol. Cell 26(2), 294–304 (2015). doi:10.1091/
mbc.E14-09-1367
9 Structural Biology in Situ Using Cryo-Electron …
257
cryoelectron subtomograms. Structure 22(10), 1528–1537 (2014). doi:10.1016/j.str.2014.08.
007
23. T.A. Steitz, A structural understanding of the dynamic ribosome machine. Nat. Rev. Mol. Cell
Biol. 9(3), 242–253 (2008). doi:10.1038/nrm2352
24. F. Brandt, L.A. Carlson, F.U. Hartl, W. Baumeister, K. Grunewald, The three-dimensional
organization of polyribosomes in intact human cells. Mol. Cell 39(4), 560–569 (2010). doi:10.
1016/j.molcel.2010.08.003
25. F. Brandt, S.A. Etchells, J.O. Ortiz, A.H. Elcock, F.U. Hartl, W. Baumeister, The native 3D
organization of bacterial polysomes. Cell 136(2), 261–271 (2009). doi:10.1016/j.cell.2008.11.
016
26. A.G. Myasnikov, Z.A. Afonina, J.F. Menetret, V.A. Shirokov, A.S. Spirin, B.P. Klaholz, The
molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes.
Nat. Commun. 5, 5294 (2014). doi:10.1038/ncomms6294
27. Z.A. Afonina, A.G. Myasnikov, V.A. Shirokov, B.P. Klaholz, A.S. Spirin, Formation of
circular polyribosomes on eukaryotic mRNA without cap-structure and poly(A)-tail: a cryo
electron tomography study. Nucleic Acids Res. 42(14), 9461–9469 (2014). doi:10.1093/nar/
gku599
28. Z.A. Afonina, A.G. Myasnikov, V.A. Shirokov, B.P. Klaholz, A.S. Spirin, Conformation
transitions of eukaryotic polyribosomes during multi-round translation. Nucleic Acids Res. 43
(1), 618–628 (2015). doi:10.1093/nar/gku1270
29. J.O. Ortiz, F. Brandt, V.R. Matias, L. Sennels, J. Rappsilber, S.H. Scheres, M. Eibauer, F.U.
Hartl, W. Baumeister, Structure of hibernating ribosomes studied by cryoelectron tomography
in vitro and in situ. J. Cell Biol. 190(4), 613–621 (2010). doi:10.1083/jcb.201005007
30. S. Pfeffer, F. Brandt, T. Hrabe, S. Lang, M. Eibauer, R. Zimmermann, F. Forster, Structure
and 3D arrangement of endoplasmic reticulum membrane-associated ribosomes. Structure 20
(9), 1508–1518 (2012). doi:10.1016/j.str.2012.06.010
31. S. Pfeffer, J. Dudek, M. Gogala, S. Schorr, J. Linxweiler, S. Lang, T. Becker, R. Beckmann,
R. Zimmermann, F. Forster, Structure of the mammalian oligosaccharyl-transferase complex
in the native ER protein translocon. Nat. Commun. 5, 3072 (2014). doi:10.1038/ncomms4072
32. S. Pfeffer, L. Burbaum, P. Unverdorben, M. Pech, Y. Chen, R. Zimmermann, R. Beckmann,
F. Forster, Structure of the native Sec61 protein-conducting channel. Nat. Commun. 6, 8403
(2015). doi:10.1038/ncomms9403
33. S. Pfeffer, M.W. Woellhaf, J.M. Herrmann, F. Forster, Organization of the mitochondrial
translation machinery studied in situ by cryoelectron tomography. Nat. Commun. 6, 6019
(2015). doi:10.1038/ncomms7019
34. P. Unverdorben, F. Beck, P. Sledz, A. Schweitzer, G. Pfeifer, J.M. Plitzko, W. Baumeister,
F. Forster, Deep classification of a large cryo-EM dataset defines the conformational
landscape of the 26S proteasome. Proc. Natl. Acad. Sci. U.S.A. 111(15), 5544–5549 (2014).
doi:10.1073/pnas.1403409111
35. T. Movassagh, K.H. Bui, H. Sakakibara, K. Oiwa, T. Ishikawa, Nucleotide-induced global
conformational changes of flagellar dynein arms revealed by in situ analysis. Nat. Struct. Mol.
Biol. 17(6), 761–767 (2010). doi:10.1038/nsmb.1832
36. J. Lin, K. Okada, M. Raytchev, M.C. Smith, D. Nicastro, Structural mechanism of the dynein
power stroke. Nat. Cell Biol. 16(5), 479–485 (2014). doi:10.1038/ncb2939
37. G. Pigino, K.H. Bui, A. Maheshwari, P. Lupetti, D. Diener, T. Ishikawa, Cryoelectron
tomography of radial spokes in cilia and flagella. J. Cell Biol. 195(4), 673–687 (2011). doi:10.
1083/jcb.201106125
38. T. Oda, H. Yanagisawa, M. Kikkawa, Detailed structural and biochemical characterization of
the nexin-dynein regulatory complex. Mol. Biol. Cell 26(2), 294–304 (2015). doi:10.1091/
mbc.E14-09-1367
9 Structural Biology in Situ Using Cryo-Electron …
257