|Entry||Database: PDB / ID: 2i68|
|Title||Cryo-EM based theoretical model structure of transmembrane domain of the multidrug-resistance antiporter from E. coli EmrE|
|Keywords||TRANSPORT PROTEIN / transmembrane protein / small-multidrug resistance / transporter / homodimer / dual topology|
|Specimen source||Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /|
|Method||Electron crystallography (7.5 Å resolution / 2d array / Crystallography)|
|Authors||Fleishman, S.J. / Harrington, S.E. / Enosh, A. / Halperin, D. / Tate, C.G. / Ben-Tal, N.|
|Citation||J. Mol. Biol., 2006, 364, 54-67|
primary. J. Mol. Biol., 2006, 364, 54-67 Yorodumi Papers
#1. Embo J., 2003, 22, 6175-6181 Yorodumi Papers
SummaryFull reportAbout validation report
|Date||Deposition: Aug 28, 2006 / Release: Oct 3, 2006|
Downloads & links
A: Protein emrE
B: Protein emrE
Mass: 15203.710 Da / Num. of mol.: 2
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P23895
|Experiment||Method: ELECTRON CRYSTALLOGRAPHY|
|EM experiment||Aggregation state: 2D ARRAY / Reconstruction method: CRYSTALLOGRAPHY|
|Component||Name: multidrug-resistance antiporter from E. coli EmrE / Type: COMPLEX|
|Buffer solution||Details: 20 mM Sodium phosphate pH7.5, 100 mM NaCl, 2mM / pH: 7.5|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: NITROGEN|
Model: Tecnai F30 / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TECNAI F30 / Date: Jan 1, 2003|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN|
|Electron lens||Mode: BRIGHT FIELD / Nominal magnification: 60000 / Nominal defocus max: 1600 nm / Nominal defocus min: 200 nm|
|Image recording||Electron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM|
|Radiation||Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: electron|
|Radiation wavelength||Relative weight: 1|
|3D reconstruction||Resolution: 7.5 Å / Resolution method: OTHER|
Details: Canonical alpha-helices were fitted into a cryo-EM structure of EmrE at 6Angstroms in-plane and 16Angstroms vertical resolution. The sequence segments were assigned based on biophysical and sequence data as elaborated in the principal citation. The orientation of each helix around its principal axis was set using evolutionary conservation, requiring that evolutionarily conserved positions be packed inside the core of the protein, whereas variable residues face the outside. A kink was introduced in helix C to fit a bend in the cryo-EM structure and according to sequence clues (see principal citation). A full description of potential inaccuracies in the model is presented in the principal citation. In brief, these include the following: the vertical positioning of the helices may be wrong by several Angstroms due to the low vertical resolution of the cryo-EM structure; the orientations of the helices around their principal axes may vary by about 20 degrees; the positions of backbone atoms on the terminal turns of each helix may not conform to alpha-helical ideality as assumed in the model structure.
Symmetry type: 2D CRYSTAL
|Number of atoms included #LAST||Protein: 624 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 624|
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