REL OBS RCSB RCSB RCSB 2014-08-19 2014-09-24 2015-09-02 2015-09-02 2015-09-02 Imaging proteins and cells in liquid solution at nanometer resolution by electron microscopy Ren G Peng B Zhang L Lei D Lu Z Wong E Zhang M Rames MJ Liu J De Yoreo JJ Zhang J Liquid-cell transmission electron microscopy, protein structure in liquid solution, bacteria structure in growth medium, virus infecting mammalian cell Ren G Peng B Zhang L Lei D Lu Z Wong E Zhang M Rames MJ Liu J De Yoreo JJ Zhang J Imaging proteins and cells in liquid solution at nanometer resolution by electron microscopy To Be Published Zhang L Ren G IPET and FETR: Experimental Approach for Studying Molecular Structure Dynamics by Cryo-Electron Tomography of a Single-Molecule Structure PLOS ONE 7 e30249 e30249 2012 22291925 doi:10.1371/journal.pone.0030249 An HIV-like virus in the "landing" stage of infecting a HeLa cell. Images were acquired in liquid solution by electron microscopy, and the 3D reconstruction was performed using IPET. An HIV-like virus in the "landing" stage of infecting a HeLa cell. Images were acquired in liquid solution by electron microscopy, and the 3D reconstruction was performed using IPET.
The lentivirus is a replication-incompetent HIV that was generated using a third-generation packaging system for the expression of non-functional short hairpin RNA.
a single HIV-like virus bound to the surface membrane of a HeLa cell 2 Lentivirus
A HIV-like virus infecting a HeLa cell surface.
Lentivirus Homo sapiens VERTEBRATES VIRUS-LIKE PARTICLE OTHER true false replication-incompetent HIV surface membrane false Homo sapiens human HeLa cell tomography cell 7.4
MEM medium (containing 10% FBS with 5% CO2)
 NEGATIVE
No stain, in liquid solution, at room temperature
Two 200 mesh copper TEM grids pre-coated with a thin layer of Formvar film, no glow discharge
 NONE OTHER ZEISS LIBRA120PLUS FLOOD BEAM BRIGHT FIELD LAB6 120 2.2 11.0 10000.0 13988.0 OTHER 293 296 295 Objective lens astigmatism was corrected at 125,000 times magnification. Zeiss Libra 120 PLUS 0.0 20.0
Low-dose illumination
2010-11-15 GATAN ULTRASCAN 4000 (4k x 4k) 103 26 16.0 Normal room-temperature specimen holder -36 66 1
Whole micrographs were initially aligned using the IMOD software package. CTF was then corrected using TOMOCTF. Small areas within the images (square windows of 128 to 360 pixels, i.e., ~137 to 386 nm) containing the targeted virus were tracked, selected, windowed, aligned, and refined using individual-particle electron tomography (IPET) software.
OTHER 73.0 OTHER IPET, Spider, EMAN, TOMOCTF, IMOD
The resolution was defined based on intra-Fourier shell correlation, in which the aligned images were split into two halves (odd index or even index) to generate two 3D reconstructions for computing FSC curves against spatial frequency shells in Fourier space. The frequency at which the FSC curve falls to a value of 0.5 was used to represent the resolution of the IPET 3D density map.
103
TOMOCTF
 emd_6039.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 -180 -180 -180 360 360 360 3859.2002 3859.2002 3859.2002 90.0 90.0 90.0 X Y Z -1.516608 1.0405004 0.0063672 0.07338254 10.72 10.72 10.72 3D reconstruction of an HIV-like particle landing on the membrane surface of a HeLa cell in liquid solution. The particle was imaged in liquid solution and the 3D reconstruction was performed using IPET (Individual-Particle Electron Tomography).
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emd_6039.tif