Journal Club

Cryo-EM Method Developments and Applications

Time: 3-5PM Fridays

Room: Hock 147

Date

Presenter

Topic and Papers

2016-04-08

Kunpeng Li

Development of Phase-plate in TEM   PPT

  1. Kuniaki Nagayama,JEM,2011,doi: 10.1093/jmicro/dfr037
  2. Robert M. Glaeser,2013, Review paper, http://dx.doi.org/10.1063/1.4830355
  3. Danev, R., Buijsse, B., Khoshouei, M., Plitzko, J. M. & Baumeister, W. PNAS 111, 15635–15640 (2014), doi: 10.1073/pnas.1418377111
  4. Fukuda Y, Laugks U, Lučić V, Baumeister W, Danev R. 2015. JSB 190:143-154. doi: 10.1016/j.jsb.2015.03.004
  5. Radostin Danev, Wolfgang Baumeister, elife 2016, DOI: http://dx.doi.org/10.7554/eLife.13046
  6.  Maryam Khoshouei,et al,Wolfgang Baumeister,Radostin Danev, Nature Communications 2016, doi:10.1038/ncomms10534

2016-03-11

Guimei Yu

Atomic Modeling from Cryo-EM Map: automatic de novo modeling and model validation

PDF

  1. Barad, B.A. et al. EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. Nature methods 12, 943-6 (2015).
  2. Chen, V.B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta crystallographica. Section D, Biological crystallography 66, 12-21 (2010).
  3. Wang, R.Y. et al. De novo protein structure determination from near-atomic-resolution cryo-EM maps. Nature methods 12, 335-8 (2015).

2016-02-12

Rui Yan

Hybrid of single particle analysis and cryo-ET in data collection and image processing

PPT

  1. Bharat TA, et al. (2012) Structure of the immature retroviral capsid at 8 Å resolution by cryo-electron microscopy. Nature 487(7407):385–389.
  2. Bharat TA, et al. (2014) Cryo-electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. Proc. Natl. Acad. Sci. USA, 111, 8233–8238
  3. Briggs JA, et al. Structure and assembly of immature HIV. Proc. Natl. Acad. Sci. USA 2009, 106, 11090–11095.

2016-01-22

Wen Jiang

Parallel processing

PDF

2016-01-15

Kunpeng Li

Anisotropic magnification distortion

PPT   Lens-Current-of-Titan-CM200

  1. J. Baldwin, R. Henderson, Measurement and evaluation of electron diffraction patterns from two-dimensional crystals, Ultramicroscopy 14 (4) (1984) 319–335.
  2. Grant, T., Grigorieff, N., 2015. Automatic estimation and correction of anisotropic magnification distortion in electron microscopes. J. Struct. Biol. doi:10.1016/j.jsb.2015.08.006
  3. Enrico Mugnaioli, Giancarlo Capitani, Fernando Nieto, Marcello Mellini, Accurate and precise lattice parameters by selected-area electron diffraction in the transmission electron microscope,American Mineralogist. Volume 94, Issue 5-6, Pages 793–800
  4. A method to correct elliptical distortion of diffraction patterns in TEM,Microscopy and Microanalysis,Volume 14 ,S2,August 2008, pp 1126-1127
  5. Kaynig, V., Fischer, B., Müller, E., Buhmann, J. M., Fully Automatic Stitching and Distortion Correction of Transmission Electron Microscope Images , Journal of Structural Biology, 171(2), August 2010, 163-173.
  6. Patent: US 2013/0062520, Henstra,2013.3: DISTORTION FREE STIGMATION OF A TEM https://www.google.com/patents/US8569693
  7. Zhao, J., Brubaker, M.A., Benlekbir, S., Rubinstein, J.L., 2015. Description and comparison of algorithms for correcting anisotropic magnification in cryo-EM images. J. Struct. Biol. 192, 209–215. doi:10.1016/j.jsb.2015.06.014
  8. Capitani, G.C., Oleynikov, P., Hovmöller, S., Mellini, M., 2006. A practical method to detect and correct for lens distortion in the TEM. Ultramicroscopy 106, 66–74. doi:10.1016/j.ultramic.2005.06.003

2015-12-11

Frank Vago

Tilt Pair: initial models and validation

  1. Henderson, R., Chen, S., Chen, J.Z., Grigorieff, N., Passmore, L.A., Ciccarelli, L., Rubinstein, J.L., Crowther, R.A., Stewart, P.L., Rosenthal, P.B., 2011. Tilt-pair analysis of images from a range of different specimens in single-particle electron cryomicroscopy. J. Mol. Biol. 413, 1028–1046. doi:10.1016/j.jmb.2011.09.008
  2. Rosenthal, P.B., Henderson, R., 2003. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745. doi:10.1016/j.jmb.2003.07.013
  3. Yoshioka, C., Pulokas, J., Fellmann, D., Potter, C.S., Milligan, R.A., Carragher, B., 2007. Automation of random conical tilt and orthogonal tilt data collection using feature-based correlation. J. Struct. Biol. 159, 335–346. doi:10.1016/j.jsb.2007.03.005
  4. Leschziner, A.E., Nogales, E., 2006. The orthogonal tilt reconstruction method: an approach to generating single-class volumes with no missing cone for ab initio reconstruction of asymmetric particles. J. Struct. Biol. 153, 284–299. doi:10.1016/j.jsb.2005.10.012