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    - PDB-2i68: Cryo-EM based theoretical model structure of transmembrane domain... -

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    Basic information

    Entry
    Database: PDB / ID: 2i68
    TitleCryo-EM based theoretical model structure of transmembrane domain of the multidrug-resistance antiporter from E. coli EmrE
    DescriptorProtein emrE
    KeywordsTRANSPORT PROTEIN / transmembrane protein / small-multidrug resistance / transporter / homodimer / dual topology
    Specimen sourceEscherichia coli / bacteria /
    MethodElectron crystallography (Crystallography / Vitreous ice (cryo EM))
    AuthorsFleishman, S.J. / Harrington, S.E. / Enosh, A. / Halperin, D. / Tate, C.G. / Ben-Tal, N.
    CitationJ. Mol. Biol., 2006, 364, 54-67

    primary. J. Mol. Biol., 2006, 364, 54-67 StrPapers
    Quasi-symmetry in the cryo-EM structure of EmrE provides the key to modeling its transmembrane domain.
    Sarel J Fleishman / Susan E Harrington / Angela Enosh / Dan Halperin / Christopher G Tate / Nir Ben-Tal

    #1. Embo J., 2003, 22, 6175-6181 StrPapers
    Three-dimensional structure of the bacterial multidrug transporter EmrE shows it is an asymmetric homodimer
    Ubarretxena-Belandia, I. / Baldwin, J.M. / Schuldiner, S. / Tate, C.G.

    DateDeposition: Aug 28, 2006 / Release: Oct 3, 2006 / Last modification: Feb 24, 2009

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    Assembly

    Deposited unit
    A: Protein emrE
    B: Protein emrE

    30.4 kDa, 2 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    30,4082
    Polyers30,4082
    Non-polymers00
    Water0

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    #1idetical with deposited unit / defined by author / Symmetry operations: (identity)x1
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    Components

    #1polypeptide(L) / Protein emrE / Methyl viologen resistance protein C, Ethidium resistance protein / Source: Escherichia coli (gene. exp.) / References: UniProt: P23895

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    Experimental details

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    Experiment

    ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
    EM experimentReconstruction method: CRYSTALLOGRAPHY / Specimen type: VITREOUS ICE (CRYO EM)

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    Sample preparation

    Assembly of specimenAggregation state: 2D CRYSTAL

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    Data collection

    RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
    Radiation wavelengthRelative weight: 1

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    Processing

    3D reconstructionDetails: 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.
    Number of atoms included #LASTProtein: 624 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 624

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