PDB-2i68: Cryo-EM based theoretical model structure of transmembr... - EM Navigator

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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

Movie

Orientation:

#1: Depositted structure unit, Made by Jmol

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

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 2i68
Title	Cryo-EM based theoretical model structure of transmembrane domain of the multidrug-resistance antiporter from E. coli EmrE
Descriptor	Protein emrE
Keywords	TRANSPORT PROTEIN, transmembrane protein, small-multidrug resistance, transporter, homodimer, dual topology
Authors	Fleishman, S.J., Harrington, S.E., Enosh, A., Halperin, D., Tate, C.G., Ben-Tal, N.
Date	Deposition: 2006-08-28, Release: 2006-10-03
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: Superimposing with EM 3D map: EMDB-1087, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1087 Fit Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-4ard PDB-2r1c List of similar structure data about Omokage system

Article
Citation - primary
Article	J. Mol. Biol., Vol. 364, Issue 1, Page 54-67, Year 2006
Title	Quasi-symmetry in the cryo-EM structure of EmrE provides the key to modeling its transmembrane domain.
Authors	Sarel 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.
Keywords	Amino 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
Links	PII: S0022-2836(06)01129-6, DOI: 10.1016/j.jmb.2006.08.072, PubMed: 17005200
Citation - 1
Article	EMBO J., Vol. 22, Issue 23, Page 6175-81, Year 2003
Title	Three-dimensional structure of the bacterial multidrug transporter EmrE shows it is an asymmetric homodimer.
Authors	Iban Ubarretxena-Belandia, Joyce M Baldwin, Shimon Schuldiner, Christopher G Tate MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
Keywords	Antiporters (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
Links	PubMed: 14633977, DOI: 10.1093/emboj/cdg611, PMC: PMC291852

Components
ID 1 : Methyl viologen resistance protein C, Ethidium resistance protein
Image
Description	Protein emrE
Type	polymer
Formula weight	15203.833 Da
Number of molecules	2
Source	Method: 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
Links	UniProt: P23895, Sequence view

Sample
Assembly
Aggregation state	2D CRYSTAL
Experiment
Reconstruction method	CRYSTALLOGRAPHY
Specimen type	VITREOUS ICE (CRYO EM)

Electron Microscopy

Processing
3D reconstruction
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.
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Total atoms	624
Protein atoms	624

PDB format

All

pdb2i68.ent (uncompressed file)

Header only

mmCIF format

mmCIF

XML format

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No-atom

2i68-noatom.xml.gz

Ext-atom

2i68-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