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Cryo-EM based theoretical model structure of transmembrane domain of the multidrug-resistance antiporter from E. coli EmrE

by electron crystallography, at 7.5 A resolution

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-1087, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 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
AuthorsFleishman, S.J., Harrington, S.E., Enosh, A., Halperin, D., Tate, C.G., Ben-Tal, N.
DateDeposition: 2006-08-28, Release: 2006-10-03
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-1087, Image by UCSF CHIMERA

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Article
Citation - primary
ArticleJ. Mol. Biol., Vol. 364, Issue 1, Page 54-67, Year 2006
TitleQuasi-symmetry in the cryo-EM structure of EmrE provides the key to modeling its transmembrane domain.
AuthorsSarel J Fleishman, Susan E Harrington, Angela Enosh, Dan Halperin, Christopher G Tate, Nir Ben-Tal
Department of Biochemistry, George S Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv, Israel.
KeywordsAmino Acid Sequence, Antiporters (chemistry), Cryoelectron Microscopy, Drug Resistance, Multiple, Bacterial, EmrE protein, E coli (147995-06-0), Escherichia coli (chemistry), Escherichia coli Proteins (chemistry), Models, Molecular, Molecular Sequence Data, Protein Structure, Tertiary, Sequence Alignment
LinksPII: S0022-2836(06)01129-6, DOI: 10.1016/j.jmb.2006.08.072, PubMed: 17005200
Citation - 1
ArticleEMBO J., Vol. 22, Issue 23, Page 6175-81, Year 2003
TitleThree-dimensional structure of the bacterial multidrug transporter EmrE shows it is an asymmetric homodimer.
AuthorsIban Ubarretxena-Belandia, Joyce M Baldwin, Shimon Schuldiner, Christopher G Tate
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
KeywordsAntiporters (chemistry), Bacterial Proteins (chemistry), Biological Transport, Crystallography, X-Ray (methods), Dimerization, EmrE protein, E coli (147995-06-0), Escherichia coli (metabolism), Escherichia coli Proteins, Image Processing, Computer-Assisted, Membrane Proteins (chemistry), Models, Biological, Models, Molecular, Protein Conformation, Protein Structure, Secondary
LinksPubMed: 14633977, DOI: 10.1093/emboj/cdg611, PMC: PMC291852
Components
ID 1 : Methyl viologen resistance protein C, Ethidium resistance protein
Image
DescriptionProtein emrE
Typepolypeptide(L)
Formula weight15203.833 Da
Number of molecules2
ID1
SourceMethod: Isolated from a genetically manipulated source
Gene: Escherichia, emrE, EB, mvrC, ID:562, Escherichia coli
Host: Escherichia, ID:562, Escherichia coli

, TA15(pGp1-2), plasmid
Plasmid name: T7-7
LinksUniProt: P23895, Sequence view
Sample
Assembly
Aggregation state2D CRYSTAL
Experiment
Reconstruction methodCRYSTALLOGRAPHY
Specimen typeVITREOUS ICE (CRYO EM)
Experiment
MethodELECTRON CRYSTALLOGRAPHY
Electron Microscopy
Processing
3D reconstruction
DetailsCanonical 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.
Refine hist
Cycle idLAST
Refine idELECTRON CRYSTALLOGRAPHY
Total atoms624
Protein atoms624
Download
PDB format
Allpdb2i68.ent.gz
pdb2i68.ent (uncompressed file)
Header onlypdb2i68.ent.gz
mmCIF format
mmCIF2i68.cif.gz
XML format
All2i68.xml.gz
No-atom2i68-noatom.xml.gz
Ext-atom2i68-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.7 MB
.webm (WebM/VP8 format), 3.6 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.7 MB