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

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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 / エシェリキア・コリ, 大腸菌 /
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


Theoretical massNumber of molelcules
Total (without water)30,4082
Polyers30,4082
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
gamma
alpha
beta
Length a, b, c (A): 1.000, 1.000, 1.000 / Angle α, β, γ (deg.): 90.00, 90.00, 90.00

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Components

#1: Polypeptide(L)Protein emrE / Methyl viologen resistance protein C / Ethidium resistance protein


Mass: 15203.833 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

Cellular component

Molecular function

Biological process

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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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