, eukaryotic mRNA without cap-structure and poly(A)-tail: a cryo electron tomography study, Nucleic Acids Res, vol.42, pp.9461-9469

P. V. Afonine, R. W. Grosse-kunstleve, N. Echols, J. J. Headd, N. W. Moriarty et al., Toward automated crystallographic structure refinement with phenix.refine, Acta Cryst, vol.68, pp.352-367, 2012.

M. Allegretti, D. J. Mills, G. Mcmullan, W. Kühlbrandt, and J. Vonck, Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector, Elife, vol.3, p.1963, 2014.

L. Andronov, Y. Lutz, J. Vonesch, and B. P. Klaholz, SharpViSu: integrated analysis and segmentation of super-resolution microscopy data, Bioinformatics, vol.32, pp.2239-2241, 2016.

L. Andronov, I. Orlov, Y. Lutz, J. Vonesch, and B. P. Klaholz, ClusterViSu, a method for clustering of protein complexes by Voronoi tessellation in super-resolution microscopy, Sci. Rep, vol.6, p.24084, 2016.

J. Arnold, J. Mahamid, V. Lucic, A. De-marco, J. J. Fernandez et al., Site-Specific Cryo-focused Ion Beam Sample Preparation Guided by 3D Correlative Microscopy, Biophys. J, vol.110, pp.860-869, 2016.

S. Asano, B. D. Engel, and W. Baumeister, Situ Cryo-Electron Tomography: A Post-Reductionist Approach to Structural Biology, vol.428, pp.332-343, 2016.

X. C. Bai, I. S. Fernandez, G. Mcmullan, and S. H. Scheres, Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles, vol.2, p.461, 2013.

N. J. Baird, S. J. Ludtke, H. Khant, W. Chiu, T. Pan et al., Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy, J. Am. Chem. Soc, vol.132, pp.16352-163523, 2010.

S. Banerjee, A. Bartesaghi, A. Merk, P. Rao, S. L. Bulfer et al., ) 2.3Å resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition, Science, vol.351, pp.871-875, 2016.

B. A. Barad, N. Echols, R. Y. Wang, Y. Cheng, F. Dimaio et al., EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy, Nat. Methods, vol.12, pp.943-946, 2015.

M. Beck, F. Förster, M. Ecke, J. M. Plitzko, F. Melchior et al., Nuclear pore complex structure and dynamics revealed by cryoelectron tomography, Science, vol.306, pp.1387-1390, 2004.

B. Beinsteiner, J. Michalon, and B. P. Klaholz, IBiSS, a versatile and interactive tool for integrated sequence and 3D structure analysis of large macromolecular complexes, Bioinformatics, vol.31, pp.3339-3344, 2015.

A. Ben-shem, L. Jenner, G. Yusupova, and M. Yusupov, Crystal structure of the eukaryotic ribosome, Science, vol.330, pp.1203-1209, 2010.

F. Brandt, L. A. Carlson, F. U. Hartl, W. Baumeister, and K. Grünewald, The three-dimensional organization of polyribosomes in intact human cells, Mol. Cell, vol.39, pp.560-569, 2010.

J. A. Briggs, Structural biology in situ -the potential of subtomogram averaging, Curr. Opin. Struct. Biol, vol.23, pp.261-267, 2013.

A. F. Brilot, J. Z. Chen, A. Cheng, J. Pan, S. C. Harrison et al., Beam-induced motion of vitrified specimen on holey carbon film, J. Struct. Biol, vol.177, pp.630-637, 2012.

C. Broennimann, E. F. Eikenberry, B. Henrich, R. Horisberger, G. Huelsen et al., The PILATUS 1M detector, J. Synchrotron Radiat, vol.13, pp.120-130, 2006.

A. Brown, F. Long, R. A. Nicholls, J. Toots, P. Emsley et al., Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions, Acta Crystallogr. D Biol. Crystallogr, vol.71, pp.136-153, 2015.

M. G. Campbell, A. Cheng, A. F. Brilot, A. Moeller, D. Lyumkis et al., Movies of ice-embedded particles enhance resolution in electron cryo-microscopy, Structure, vol.20, pp.1823-1828, 2012.

J. M. Carazo, C. O. Sorzano, J. Otón, R. Marabini, and J. Vargas, Three-dimensional reconstruction methods in Single Particle Analysis from transmission electron microscopy data, Arch. Biochem. Biophys, vol.581, pp.39-48, 2015.

M. Carroni and H. R. Saibil, Cryo electron microscopy to determine the structure of macromolecular complexes, Methods, vol.95, pp.78-85, 2016.

A. Casanas, R. Warshamanage, A. D. Finke, E. Panepucci, V. Olieric et al., EIGER detector: application in macromolecular crystallography, Acta Crystallogr. D Struct. Biol, vol.72, pp.1036-1048, 2016.

D. Castaño-díez, M. Kudryashev, and H. Stahlberg, Dynamo Catalogue: Geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms, J. Struct. Biol, vol.16, pp.30111-30113, 2016.

Y. W. Chang, L. A. Rettberg, A. Treuner-lange, J. Iwasa, L. Søgaard-andersen et al., Architecture of the type IVa pilus machine, Science, vol.351, p.2001, 2016.

B. Chen, S. Kaledhonkar, M. Sun, B. Shen, Z. Lu et al., Structural dynamics of ribosome subunit association studied by mixing-spraying time-resolved cryogenic electron microscopy, Structure, vol.23, pp.1097-1105, 2015.

J. Z. Chen, E. C. Settembre, S. T. Aoki, X. Zhang, A. R. Bellamy et al., Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM, Proc. Natl. Acad. Sci. U.S.A, vol.106, pp.10644-10648, 2009.

Y. Chen, S. Pfeffer, J. J. Fernández, C. O. Sorzano, and F. Förster, Autofocused 3D classification of cryoelectron subtomograms, Structure, vol.22, pp.1528-1537, 2014.

E. Y. Chua, V. K. Vogirala, O. Inian, A. S. Wong, L. Nordenskiöld et al., ) 3.9Å structure of the nucleosome core particle determined by phase-plate cryo-EM, Nucleic Acids Res, vol.44, pp.8013-8019, 2016.

W. Dai, C. Fu, H. A. Khant, S. J. Ludtke, M. F. Schmid et al., Zernike phase-contrast electron cryotomography applied to marine cyanobacteria infected with cyanophages, Nat. Protoc, vol.9, pp.2630-2642, 2014.

R. Danev and W. Baumeister, Cryo-EM single particle analysis with the Volta phase plate, Elife, vol.5, p.13046, 2016.

R. Danev, B. Buijsse, M. Khoshouei, J. M. Plitzko, and W. Baumeister, Volta potential phase plate for in-focus phase contrast transmission electron microscopy, Proc. Natl Acad. Sci. U.S.A, vol.44, pp.15635-15640, 2014.

J. Dubochet, M. Adrian, J. J. Chang, J. C. Homo, J. Lepault et al., Cryo-electron microscopy of vitrified specimens, Q. Rev. Biophys, vol.21, pp.129-228, 1988.

A. Dubrovsky, S. Sorrentino, J. Harapin, K. Sapra, T. Medalia et al., Developments in cryo-electron tomography for in situ structural analysis, Arch. Biochem. Biophys, vol.581, pp.78-85, 2015.

N. V. Dudkina, R. Kouril, J. B. Bultema, and E. J. Boekema, Imaging of organelles by electron microscopy reveals protein-protein interactions in mitochondria and chloroplasts, FEBS Lett, vol.584, pp.2510-2515, 2010.

L. A. Earl and S. Subramaniam, Cryo-EM of viruses and vaccine design, Proc. Nat. Acad. Sci. U.S.A, vol.113, pp.8903-8905, 2016.

D. Eiler, J. Lin, A. Simonetti, B. P. Klaholz, and T. A. Steitz, IF2 Initiation factor 2 crystal structure reveals a different domain organization from eukaryotic initiation factor 5B and mechanism among translational GTPases, Proc. Nat. Acad. Sci. U.S.A, vol.110, pp.15662-15667, 2013.

P. Emsley, B. Lohkamp, W. G. Scott, and K. Cowtan, Features and development of Coot, Acta Crystallogr. D Biol. Crystallogr, vol.66, pp.486-501, 2010.

N. Fischer, A. L. Konevega, W. Wintermeyer, M. V. Rodnina, and H. Stark, Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy, Nature, vol.466, pp.329-333, 2010.

N. Fischer, P. Neumann, A. L. Konevega, L. V. Bock, R. Ficner et al., Structure of the E. coli ribosome-EF-Tu complex at <3Å resolution by Cs-corrected cryo-EM, Nature, vol.520, pp.567-570, 2015.

A. S. Frangakis, J. Böhm, F. Förster, S. Nickell, D. Nicastro et al., Identification of macromolecular complexes in cryoelectron tomograms of phantom cells, Proc. Natl. Acad. Sci. U.S.A, vol.99, pp.14153-14158, 2002.

G. A. Frank, A. Bartesaghi, O. Kuybeda, M. J. Borgnia, T. A. White et al., Computational separation of conformational heterogeneity using cryo-electron tomography and 3D sub-volume averaging, J. Struct. Biol, vol.178, pp.165-176, 2012.

N. Frindt, M. Oster, S. Hettler, B. Gamm, L. Dieterle et al., In-focus electrostatic Zach phase plate imaging for transmission electron microscopy with tunable phase contrast of frozen hydrated biological samples, Microsc. Microanal, vol.1, pp.175-183, 2014.

J. Fu, H. Gao, and J. Frank, Unsupervised classification of single particles by cluster tracking in multi-dimensional space, J. Struct. Biol, vol.157, pp.226-239, 2006.

J. G. Galaz-montoya, C. W. Hecksel, P. R. Baldwin, E. Wang, S. C. Weaver et al., Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography, J. Struct. Biol, vol.194, pp.383-394, 2016.

H. Gao, M. Valle, M. Ehrenberg, and J. Frank, Dynamics of EF-G interaction with the ribosome explored by classification of a heterogeneous cryo-EM dataset, J. Struct. Biol, vol.147, pp.283-290, 2004.

R. M. Glaeser, Protein complexes in focus, Elife, vol.5, 2016.

T. Grant and N. Grigorieff, Measuring the optimal exposure for single particle cryo-EM using a 2.6Å reconstruction of rotavirus VP6, vol.4, p.6980, 2015.

B. J. Greber, P. Bieri, M. Leibundgut, A. Leitner, R. Aebersold et al., The complete structure of the 55S mammalian mitochondrial ribosome, Science, vol.348, pp.303-308, 2015.

C. Hagen, K. C. Dent, T. Zeev-ben-mordehai, M. Grange, J. B. Bosse et al., Cell, vol.163, pp.1692-1701, 2015.

W. J. Hagen, W. Wan, and J. A. Briggs, Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging, J. Struct. Biol, vol.16, pp.30113-30117, 2016.

J. M. Heumann, A. Hoenger, and D. N. Mastronarde, Clustering and variance maps for cryo-electron tomography using wedge-masked differences, J. Struct. Biol, vol.175, pp.288-299, 2011.

R. N. Irobalieva, B. Martins, and O. Medalia, Cellular structural biology as revealed by cryo-electron tomography, J. Cell Sci, vol.129, pp.469-476, 2016.

M. A. Karreman, L. Mercier, N. L. Schieber, G. Solecki, G. Allio et al., Fast and precise targeting of single tumor cells in vivo by multimodal correlative microscopy, J. Cell Sci, vol.129, pp.444-456, 2016.

H. Khatter, A. G. Myasnikov, L. Mastio, I. M. Billas, C. Birck et al., Purification, characterization and crystallization of the human 80S ribosome, Nucleic Acids Res, vol.42, pp.1-11, 2014.

H. Khatter, A. G. Myasnikov, K. Natchiar, and B. P. Klaholz, Structure of the human 80S ribosome, Nature, vol.520, pp.640-645, 2015.

M. Khoshouei, S. Pfeffer, W. Baumeister, F. Förster, and R. Danev, Subtomogram analysis using the Volta phase plate, J. Struct. Biol, vol.16, pp.30103-30104, 2016.

M. Khoshouei, M. Radjainia, A. J. Phillips, J. A. Gerrard, A. K. Mitra et al., Volta phase plate cryo-EM of the small protein complex Prx3, Nat. Commun, vol.7, p.10534, 2016.

D. Kim, T. J. Deerinck, Y. M. Sigal, H. P. Babcock, M. H. Ellisman et al., Correlative stochastic optical reconstruction microscopy and electron microscopy, PLoS One, vol.10, 2015.

C. Kizilyaprak, J. Daraspe, and B. M. Humbel, Focused ion beam scanning electron microscopy in biology, J. Microsc, vol.254, pp.109-114, 2014.

B. P. Klaholz, Structure sorting of multiple macromolecular states in heterogeneous cryo-EM samples by 3D multivariate statistical analysis, Open J. Stat, vol.5, pp.820-836, 2015.

B. P. Klaholz, A. G. Myasnikov, and M. Van-heel, Visualization of release factor 3 on the ribosome during termination of protein synthesis, Nature, vol.427, pp.862-865, 2004.

R. I. Koning, K. Celler, J. Willemse, E. Bos, G. P. Van-wezel et al., Correlative cryo-fluorescence light microscopy and cryo-electron tomography of Streptomyces, Methods Cell Biol, vol.124, pp.217-239, 2014.

J. Kosinski, S. Mosalaganti, A. Von-appen, R. Teimer, A. L. Diguilio et al., Molecular architecture of the inner ring scaffold of the human nuclear pore complex, Science, vol.352, pp.363-365, 2016.

M. Kuijper, G. Van-hoften, B. Janssen, R. Geurink, S. De-carlo et al., FEI's direct electron detector developments: Embarking on a revolution in cryo-TEM, J. Struct. Biol, vol.192, pp.179-187, 2015.

W. Kunath, K. Weiss, H. Sack-kongehl, M. Kessel, and E. Zeitler, Time-resolved low-dose microscopy of glutamine synthetase molecules, Ultramicroscopy, vol.13, pp.241-252, 1984.

O. Kuybeda, G. A. Frank, A. Bartesaghi, M. Borgnia, S. Subramaniam et al., Collaborative framework for 3D alignment and classification of heterogeneous subvolumes in cryo-electron tomography, J. Struct. Biol, vol.181, pp.116-127, 2013.

R. F. Laine, A. Albecka, S. Van-de-linde, E. J. Rees, C. M. Crump et al., Structural analysis of herpes simplex virus by optical super-resolution imaging, Nat. Commun, vol.6, p.5980, 2015.

X. Li, P. Mooney, S. Zheng, C. R. Booth, M. B. Braunfeld et al., Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM, Nat. Methods, vol.10, pp.584-590, 2013.

H. Y. Liao, Y. Hashem, and J. Frank, Efficient estimation of three-dimensional covariance and its application in the analysis of heterogeneous samples in cryo-electron microscopy, Structure, vol.23, pp.1129-1237, 2015.

D. H. Lin, T. Stuwe, S. Schilbach, E. J. Rundlet, T. Perriches et al., , vol.352, p.6283, 2016.

A. Löschberger, C. Franke, G. Krohne, S. Van-de-linde, and M. Sauer, Correlative super-resolution fluorescence and electron microscopy of the nuclear pore complex with molecular resolution, J. Cell Sci, vol.127, pp.4351-4355, 2014.

V. Lu?i?, A. Rigort, and W. Baumeister, Cryo-electron tomography: the challenge of doing structural biology in situ, J. Cell Biol, vol.202, pp.407-419, 2013.

D. Lyumkis, A. F. Brilot, D. L. Theobald, and N. Grigorieff, Likelihood-based classification of cryo-EM images using FREALIGN, J. Struct. Biol, vol.183, pp.377-388, 2013.

J. Mahamid, S. Pfeffer, M. Schaffer, E. Villa, R. Danev et al., Visualizing the molecular sociology at the HeLa cell nuclear periphery, Science, vol.351, pp.969-972, 2016.

J. Mahamid, R. Schampers, H. Persoon, A. A. Hyman, W. Baumeister et al., A focused ion beam milling and lift-out approach for site-specific preparation of frozen-hydrated lamellas from multicellular organisms, J. Struct. Biol, vol.192, pp.262-269, 2015.

M. Maletta, I. M. Orlov, P. Roblin, Y. Beck, D. Moras et al., The palindromic DNA-bound USP/EcR nuclear receptor adopts an asymmetric organization with allosteric domain positioning, Nat. Commun, vol.5, p.4139, 2014.

G. Mcmullan, S. Chen, R. Henderson, and A. R. Faruqi, Detective quantum efficiency of electron area detectors in electron microscopy, Ultramicroscopy, vol.109, pp.1126-1143, 2009.

G. Mcmullan, A. R. Faruqi, D. Clare, and R. Henderson, Comparison of optimal performance at 300keV of three direct electron detectors for use in low dose electron microscopy, Ultramicroscopy, vol.147, pp.156-163, 2014.

O. Medalia, I. Weber, A. S. Frangakis, D. Nicastro, G. Gerisch et al., Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography, Science, vol.298, pp.1209-1213, 2002.

J. Ménétret, H. Khatter, A. Simonetti, I. Orlov, A. G. Myasnikov et al., Integrative structure-function analysis of large nucleoprotein complexes, 2013.

A. Merk, A. Bartesaghi, S. Banerjee, V. Falconieri, P. Rao et al., Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery, Cell, vol.165, pp.1698-1707, 2016.

J. L. Milne, M. J. Borgnia, A. Bartesaghi, E. E. Tran, L. A. Earl et al., Cryo-electron microscopy -a primer for the non-microscopist, FEBS J, vol.280, pp.28-45, 2013.

K. Murata, X. Liu, R. Danev, J. Jakana, M. F. Schmid et al., Zernike phase contrast cryo-electron microscopy and tomography for structure determination at nanometer and subnanometer resolutions, Structure, vol.18, pp.903-912, 2010.

A. G. Myasnikov, Z. A. Afonina, J. Ménétret, V. A. Shirokov, A. S. Spirin et al., The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes, Nat. Commun, vol.5, p.5294, 2014.

A. G. Myasnikov, Z. Afonina, and B. P. Klaholz, Single particle and molecular assembly analysis of polyribosomes by single-and double-tilt cryo electron tomography, Ultramicroscopy, vol.126, pp.33-39, 2013.

A. G. Myasnikov, S. K. Natchiar, M. Nebout, I. Hazemann, V. Imbert et al., Structure-function insights reveal the human ribosome as a cancer target for antibiotics, Nat. Commun, vol.7, p.12856, 2016.

A. Nans, M. Kudryashev, H. R. Saibil, and R. D. Hayward, Structure of a bacterial type III secretion system in contact with a host membrane in situ, Nat. Commun, vol.6, p.10114, 2015.

I. Nederlof, Y. W. Li, M. Van-heel, and J. P. Abrahams, Imaging protein three-dimensional nanocrystals with cryo-EM, Acta Crystallogr. D Biol. Crystallogr, vol.69, pp.852-859, 2013.

J. M. Obbineni, R. Yamamoto, and T. Ishikawa, A simple and fast approach for missing-wedge invariant classification of subtomograms extracted from filamentous structures, J. Struct. Biol, vol.16, p.30172, 2016.

I. Orlov, N. Rochel, D. Moras, and B. P. Klaholz, Structure of the full human RXR/VDR nuclear receptor heterodimer complex with its DR3 target DNA, EMBO J, vol.31, pp.291-300, 2012.

I. Orlov, A. Schertel, G. Zuber, B. P. Klaholz, R. Drillien et al., Live cell immunogold labelling of RNA polymerase II, Sci. Rep, vol.5, p.8324, 2015.

E. V. Orlova and H. R. Saibil, Methods for three-dimensional reconstruction of heterogeneous assemblies, Methods Enzymol, vol.482, pp.321-362, 2010.

J. O. Ortiz, F. Förster, J. Kürner, A. A. Linaroudis, and W. Baumeister, Mapping 70S ribosomes in intact cells by cryoelectron tomography and pattern recognition, J. Struct. Biol, vol.156, pp.334-341, 2006.

P. A. Penczek, J. Frank, and C. M. Spahn, A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation, J. Struct. Biol, vol.154, pp.184-194, 2006.

C. Rajendran, F. S. Dworkowski, M. Wang, and C. Schulze-briese, Radiation damage in room-temperature data acquisition with the PILATUS 6M pixel detector, J. Synchrotron Radiat, vol.18, pp.318-328, 2011.

P. Ray, B. P. Klaholz, R. D. Finn, E. V. Orlova, P. C. Burrows et al., Determination of Escherichia coli RNA polymerase structure by single particle cryoelectron microscopy, Methods Enzymol, vol.370, pp.24-42, 2003.

I. Razinkov, V. P. Dandey, H. Wei, Z. Zhang, D. Melnekoff et al., A new method for vitrifying samples for cryoEM, J. Struct. Biol, vol.195, pp.190-198, 2016.

D. Rhinow, Towards an optimum design for thin film phase plates, Ultramicroscopy, vol.160, pp.1-6, 2016.

A. Rigort and J. M. Plitzko, Cryo-focused-ion-beam applications in structural biology, Arch. Biochem. Biophys, vol.581, pp.122-130, 2015.

R. S. Ruskin, Z. Yu, and N. Grigorieff, Quantitative characterization of electron detectors for transmission electron microscopy, J. Struct. Biol, vol.184, pp.385-393, 2013.

M. R. Sawaya, J. Rodriguez, D. Cascio, M. J. Collazo, D. Shi et al., Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED, Proc. Natl. Acad. Sci. U.S.A, p.201606287, 2016.

M. Schaffer, J. Mahamid, B. D. Engel, T. Laugks, W. Baumeister et al., Optimized cryo-focused ion beam sample preparation aimed at in situ structural studies of membrane proteins, J. Struct. Biol, vol.16, pp.30151-30154, 2016.

S. H. Scheres, M. Valle, R. Nuez, C. O. Sorzano, R. Marabini et al., Maximum likelihood multi-reference refinement for electron microscopy images, J. Mol. Biol, vol.22, pp.139-149, 2005.

S. H. Scheres, Classification of structural heterogeneity by maximum-likelihood methods, Methods Enzymol, vol.482, pp.295-320, 2010.

S. H. Scheres, Beam-induced motion correction for sub-megadalton cryo-EM particles, Elife, vol.3, p.3665, 2014.

R. T. Schirra and P. Zhang, Correlative fluorescence and electron microscopy, Curr. Protoc. Cytom, vol.70, pp.1-10, 2014.

M. Schorb, L. Gaechter, O. Avinoam, F. Sieckmann, M. Clarke et al., New hardware and workflows for semi-automated correlative cryo-fluoresence and cryo-electron microscopy/tomography, J. Struct. Biol, vol.16, pp.30135-30136, 2016.

F. K. Schur, M. Obr, W. J. Hagen, W. Wan, A. J. Jakobi et al., An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation, Science, vol.353, pp.506-508, 2016.

D. Shi, B. L. Nannenga, M. J. De-la-cruz, J. Liu, S. Sawtelle et al., The collection of MicroED data for macromolecular crystallography, Nat. Protoc, vol.11, pp.895-904, 2016.

F. J. Sigworth, A maximum-likelihood approach to single-particle image refinement, J. Struct. Biol, vol.122, pp.328-339, 1998.

A. Simonetti, S. Marzi, A. Fabbretti, I. Hazemann, L. Jenner et al., Structure of the protein core of translation initiation factor 2 in apo, GTP-bound and GDP-bound forms, Acta Cryst, vol.69, pp.925-933, 2013.

A. Simonetti, S. Marzi, I. M. Billas, A. Tsai, A. Fabbretti et al., Involvement of IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor, Proc. Nat. Acad. Sci. U.S.A, vol.110, pp.15656-15661, 2013.

A. Simonetti, J. Ménétret, F. Martin, A. G. Myasnikov, Q. Vicens et al., Ribosomal 18S rRNA base pairs with mRNA during eukaryotic translation initiation, Nat. Commun, vol.7, p.12622, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02294260

A. Simonetti, S. Marzi, A. G. Myasnikov, A. Fabbretti, G. Yusupova et al., Structure of the 30S translation initiation complex, Nature, vol.455, pp.416-420, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00342095

O. S. Smart, T. O. Womack, C. Flensburg, P. Keller, W. Paciorek et al., Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER, Acta Crystallogr. D Biol. Crystallogr, vol.68, pp.368-380, 2012.

O. V. Sobolev, P. V. Afonine, P. D. Adams, and A. Urzhumtsev, Programming new geometry restraints: parallelity of atomic groups, J. Appl. Crystallogr, vol.48, pp.1130-1141, 2015.

J. M. Spear, A. J. Noble, Q. Xie, D. R. Sousa, M. S. Chapman et al., The influence of frame alignment with dose compensation on the quality of single particle reconstructions, J. Struct. Biol, vol.192, pp.196-203, 2015.

S. Spinelli, C. Bebeacua, I. Orlov, D. Tremblay, B. P. Klaholz et al., CryoEM structure of the lactococcal siphophage 1358 virion, J. Virol, vol.88, pp.8900-8910, 2014.

M. Stölken, F. Beck, T. Haller, R. Hegerl, I. Gutsche et al., Maximum likelihood based classification of electron tomographic data, J. Struct. Biol, vol.173, pp.77-85, 2011.

A. Szymborska, A. De-marco, N. Daigle, V. C. Cordes, J. A. Briggs et al., Nuclear pore scaffold structure analyzed by super-resolution microscopy and particle averaging, Science, vol.341, pp.655-658, 2013.

Y. Z. Tan, A. Cheng, C. S. Potter, and B. Carragher, Automated data collection in single particle electron microscopy, Microscopy (Oxf.), vol.65, pp.43-56, 2016.

M. Van-heel, B. Gowen, R. Matadeen, E. V. Orlova, R. Finn et al., Single-particle electron cryo-microscopy: towards atomic resolution, Q. Rev. Biophys, vol.33, pp.307-369, 2000.

D. Veesler, M. G. Campbell, A. Cheng, C. Y. Fu, Z. Murez et al., Maximizing the potential of electron cryomicroscopy data collected using direct detectors, J. Struct. Biol, vol.184, pp.193-202, 2013.

E. Villa, M. Schaffer, J. M. Plitzko, and W. Baumeister, Opening windows into the cell: focused-ion-beam milling for cryo-electron tomography, Curr. Opin. Struct. Biol, vol.23, pp.771-777, 2013.

A. Walter, S. Steltenkamp, S. Schmitz, P. Holik, E. Pakanavicius et al., Towards an optimum design for electrostatic phase plates, Ultramicroscopy, vol.153, pp.22-31, 2015.

W. Wan and J. A. Briggs, Cryo-electron tomography and subtomogram averaging, Methods Enzymol, vol.579, pp.329-367, 2016.

K. Wang, C. Y. Fu, R. Khayat, P. C. Doerschuk, and J. E. Johnson, In vivo virus structures: simultaneous classification, resolution enhancement, and noise reduction in whole-cell electron tomography, J. Struct. Biol, vol.174, pp.425-433, 2011.

H. E. White, H. R. Saibil, A. Ignatiou, and E. V. Orlova, Recognition and separation of single particles with size variation by statistical analysis of their images, J. Mol. Biol, vol.13, pp.453-460, 2004.

W. Wong, X. C. Bai, A. Brown, I. S. Fernandez, E. Hanssen et al., Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine. Elife 3, 2014.

M. Xu and F. Alber, Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms, Bioinformatics, vol.29, pp.274-282, 2013.

Z. Yang, K. Lasker, D. Schneidman-duhovny, B. Webb, C. C. Huang et al., UCSF Chimera, MODELLER, and IMP: an integrated modeling system, J. Struct. Biol, vol.179, pp.269-278, 2012.

J. Zhang, G. Ji, X. Huang, W. Xu, and F. Sun, An improved cryo-FIB method for fabrication of frozen hydrated lamella, J. Struct. Biol, vol.194, pp.218-223, 2016.

X. Zhang, P. Ge, X. Yu, J. M. Brannan, G. Bi et al., Cryo-EM structure of the mature dengue virus at 3.5-Å resolution, Nat. Struct. Mol. Biol, vol.20, pp.105-110, 2013.