Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	IPET and FETR: experimental approach for studying molecular structure dynamics by cryo-electron tomography of a single-molecule structure.
Journal, issue, pages	PLoS One, Vol. 7, Issue 1, Page e30249, Year 2012
Publish date	Jan 24, 2012
Authors	Lei Zhang / Gang Ren /
PubMed Abstract	The dynamic personalities and structural heterogeneity of proteins are essential for proper functioning. Structural determination of dynamic/heterogeneous proteins is limited by conventional ...The dynamic personalities and structural heterogeneity of proteins are essential for proper functioning. Structural determination of dynamic/heterogeneous proteins is limited by conventional approaches of X-ray and electron microscopy (EM) of single-particle reconstruction that require an average from thousands to millions different molecules. Cryo-electron tomography (cryoET) is an approach to determine three-dimensional (3D) reconstruction of a single and unique biological object such as bacteria and cells, by imaging the object from a series of tilting angles. However, cconventional reconstruction methods use large-size whole-micrographs that are limited by reconstruction resolution (lower than 20 Å), especially for small and low-symmetric molecule (<400 kDa). In this study, we demonstrated the adverse effects from image distortion and the measuring tilt-errors (including tilt-axis and tilt-angle errors) both play a major role in limiting the reconstruction resolution. Therefore, we developed a "focused electron tomography reconstruction" (FETR) algorithm to improve the resolution by decreasing the reconstructing image size so that it contains only a single-instance protein. FETR can tolerate certain levels of image-distortion and measuring tilt-errors, and can also precisely determine the translational parameters via an iterative refinement process that contains a series of automatically generated dynamic filters and masks. To describe this method, a set of simulated cryoET images was employed; to validate this approach, the real experimental images from negative-staining and cryoET were used. Since this approach can obtain the structure of a single-instance molecule/particle, we named it individual-particle electron tomography (IPET) as a new robust strategy/approach that does not require a pre-given initial model, class averaging of multiple molecules or an extended ordered lattice, but can tolerate small tilt-errors for high-resolution single "snapshot" molecule structure determination. Thus, FETR/IPET provides a completely new opportunity for a single-molecule structure determination, and could be used to study the dynamic character and equilibrium fluctuation of macromolecules.
External links	PLoS One / PubMed:22291925 / PubMed Central
Methods	EM (subtomogram averaging)
Resolution	14.1 - 42.0 Å
Structure data	EMDB-2021: Three-dimensional reconstructions with negative staining of a targeted individual antibody particle by individual-particle electron tomography (IPET). The reconstruction displayed three ring-shaped domains that corresponding to three domain of IgG antibody. Method: EM (subtomogram averaging) / Resolution: 14.1 Å EMDB-2022: Three-dimensional reconstruction of another targeted individual antibody particle by individual-particle electron tomography (IPET). The reconstruction displayed three ring-shaped domains that corresponding to three domain of IgG antibody. Method: EM (subtomogram averaging) / Resolution: 14.6 Å EMDB-2023: Three-dimensional reconstruction of a targeted individual 17nm nascent high-density lipoprotein (HDL) particle by individual-particle electron tomography (IPET). The reconstruction displayed a ring-shaped structure of containing three protein - apoipoprotein A-Is (28 kDa each). Method: EM (subtomogram averaging) / Resolution: 42.0 Å EMDB-2024: Three-dimensional reconstruction of another targeted individual 17nm nascent high-density lipoprotein (HDL) particle by individual-particle electron tomography (IPET). The reconstruction displayed a ring-shaped structure of containing three protein - apoipoprotein A-Is (28 kDa each). Method: EM (subtomogram averaging) / Resolution: 36.0 Å
Source	Homo sapiens (human)