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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 (7.5 Å resolution / 2d array / Crystallography)
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.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 28, 2006 / Release: Oct 3, 2006
RevisionDateData content typeGroupProviderType
1.0Oct 3, 2006Structure modelrepositoryInitial release
1.1May 1, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Assembly

Deposited unit
A: Protein emrE
B: Protein emrE


Theoretical massNumber of molelcules
Total (without water)30,4072
Polyers30,4072
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)1.000, 1.000, 1.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number1
Space group name H-MP 1

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Components

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


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

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 2D ARRAY / Reconstruction method: CRYSTALLOGRAPHY

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Sample preparation

ComponentName: multidrug-resistance antiporter from E. coli EmrE / Type: COMPLEX
Buffer solutionDetails: 20 mM Sodium phosphate pH7.5, 100 mM NaCl, 2mM / pH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: NITROGEN

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Data collection

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F30 / Date: Jan 1, 2003
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 / Nominal defocus max: 1600 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: electron
Radiation wavelengthRelative weight: 1

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Processing

3D reconstructionResolution: 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 #LASTProtein: 624 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 624

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