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PDBsum entry 3b61

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protein links
Membrane protein PDB id
3b61
Jmol
Contents
Protein chains
(+ 2 more) 107 a.a.* *
* Residue conservation analysis
* C-alpha coords only
PDB id:
3b61
Name: Membrane protein
Title: Emre multidrug transporter, apo crystal form
Structure: Multidrug transporter emre. Chain: a, b, c, d, e, f, g, h. Synonym: efflux-multidrug resistance protein emre, methyl viologen resistance protein c, ethidium resistance protein. Engineered: yes
Source: Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. Gene: emre, eb, mvrc. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
4.50Å     R-factor:   0.318     R-free:   0.362
Authors: G.Chang,Y.J.Chen
Key ref:
Y.J.Chen et al. (2007). X-ray structure of EmrE supports dual topology model. Proc Natl Acad Sci U S A, 104, 18999-19004. PubMed id: 18024586 DOI: 10.1073/pnas.0709387104
Date:
26-Oct-07     Release date:   04-Dec-07    
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P23895  (EMRE_ECOLI) -  Multidrug transporter EmrE
Seq:
Struc:
110 a.a.
107 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   4 terms 
  Biological process     transport   9 terms 
  Biochemical function     transmembrane transporter activity     5 terms  

 

 
    Key reference    
 
 
DOI no: 10.1073/pnas.0709387104 Proc Natl Acad Sci U S A 104:18999-19004 (2007)
PubMed id: 18024586  
 
 
X-ray structure of EmrE supports dual topology model.
Y.J.Chen, O.Pornillos, S.Lieu, C.Ma, A.P.Chen, G.Chang.
 
  ABSTRACT  
 
EmrE, a multidrug transporter from Escherichia coli, functions as a homodimer of a small four-transmembrane protein. The membrane insertion topology of the two monomers is controversial. Although the EmrE protein was reported to have a unique orientation in the membrane, models based on electron microscopy and now defunct x-ray structures, as well as recent biochemical studies, posit an antiparallel dimer. We have now reanalyzed our x-ray data on EmrE. The corrected structures in complex with a transport substrate are highly similar to the electron microscopy structure. The first three transmembrane helices from each monomer surround the substrate binding chamber, whereas the fourth helices participate only in dimer formation. Selenomethionine markers clearly indicate an antiparallel orientation for the monomers, supporting a "dual topology" model.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Structure determination of EmrE. (A) Experimental density for one apo EmrE monomer at 4.5-Å resolution. Anomalous Hg density (4 ), marking the positions of cysteine residues, is shown in red. The protein is shown in C^ trace and rendered in a color gradient, from green at the N terminus to yellow at the C terminus. (B) Ribbon representation of the distorted apo EmrE dimer. One monomer is rendered in color gradient with the helices labeled, and the other monomer is shown in gray. The approximate dimensions of a lipid bilayer are shown by the gray shading. (C) Views of the two apo EmrE monomers, with TM helices labeled. Note the extended configuration of the TM4 helices, which project away from the main body of the dimer. (D) Experimental density for one monomer of the EmrE-TPP complex at 3.8 Å (C2 crystal form), contoured at 1 . Anomalous Se density (3 ) is shown in red. (E) Side view of the EmrE-TPP dimer (C2 form), with the dimensions of the lipid bilayer indicated. One monomer is colored in gradient and labeled, and the other is in gray. The bound TPP is colored red. Density for the colored monomer terminates at residue 105. (F) Views of the two monomers (P2[1] form), which are essentially the same as the C2 monomers, except for the shorter TM helices, which terminate at the indicated residues. Full-length EmrE has 110 amino acid residues. Note that the superhelical twists of TM1–3 are similar in the apo and TPP-bound forms but that the helix packing interactions and monomer–monomer interactions differ.
Figure 3.
Fig. 3. EmrE binds TPP as an antiparallel dimer. (A) Stereoview of the EmrE transporter in complex with TPP. The two monomers are colored blue and yellow, and the bound TPP is pink. Anomalous Fourier density from SeMet (colored red in one monomer and green in the other) and the arsonium analogue of TPP (magenta) are shown contoured at 3 and 3.5 , respectively. The TPP and SeMet residue positions are labeled, with the two monomers distinguished by asterisks. (B) "Front" view of the transporter, emphasizing the positions of SeMet markers in TM1. The N termini of the monomers are labeled. (C) "Top" view of the EmrE-TPP structure, with the TM helices labeled. Red spheres indicate the positions of residues that have been implicated in substrate binding and transport by biochemical and mutagenesis studies (18, 20, 23–28). The only residue removed from the binding chamber is Leu-93 (TM4). In the x-ray crystals, this residue appears to mediate lattice interactions across a twofold symmetry axis relating two dimers. This crystal packing interface was also observed in the two-dimensional crystals used to derive the EM structure of EmrE-TPP (14).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22178925 E.A.Morrison, G.T.DeKoster, S.Dutta, R.Vafabakhsh, M.W.Clarkson, A.Bahl, D.Kern, T.Ha, and K.A.Henzler-Wildman (2012).
Antiparallel EmrE exports drugs by exchanging between asymmetric structures.
  Nature, 481, 45-50.  
20637904 F.Junge, S.Haberstock, C.Roos, S.Stefer, D.Proverbio, V.Dötsch, and F.Bernhard (2011).
Advances in cell-free protein synthesis for the functional and structural analysis of membrane proteins.
  N Biotechnol, 28, 262-271.  
21333528 J.D.Faraldo-Gómez, and L.R.Forrest (2011).
Modeling and simulation of ion-coupled and ATP-driven membrane proteins.
  Curr Opin Struct Biol, 21, 173-179.  
20654746 S.Rajesh, T.Knowles, and M.Overduin (2011).
Production of membrane proteins without cells or detergents.
  N Biotechnol, 28, 250-254.  
21194372 V.H.Lam, J.H.Lee, A.Silverio, H.Chan, K.M.Gomolplitinant, T.L.Povolotsky, E.Orlova, E.I.Sun, C.H.Welliver, and M.H.Saier (2011).
Pathways of transport protein evolution: recent advances.
  Biol Chem, 392, 5.  
20620041 C.J.Tsai, and C.Ziegler (2010).
Coupling electron cryomicroscopy and X-ray crystallography to understand secondary active transport.
  Curr Opin Struct Biol, 20, 448-455.  
20198639 D.Schwarz, D.Daley, T.Beckhaus, V.Dötsch, and F.Bernhard (2010).
Cell-free expression profiling of E. coli inner membrane proteins.
  Proteomics, 10, 1762-1779.  
19826804 K.McLuskey, A.W.Roszak, Y.Zhu, and N.W.Isaacs (2010).
Crystal structures of all-alpha type membrane proteins.
  Eur Biophys J, 39, 723-755.  
20667175 K.R.Vinothkumar, and R.Henderson (2010).
Structures of membrane proteins.
  Q Rev Biophys, 43, 65.  
20385730 M.Kalman, and N.Ben-Tal (2010).
Quality assessment of protein model-structures using evolutionary conservation.
  Bioinformatics, 26, 1299-1307.  
20534491 M.Schushan, Y.Barkan, T.Haliloglu, and N.Ben-Tal (2010).
C(alpha)-trace model of the transmembrane domain of human copper transporter 1, motion and functional implications.
  Proc Natl Acad Sci U S A, 107, 10908-10913.  
20407887 S.F.Poget, R.Harris, S.M.Cahill, and M.E.Girvin (2010).
1H, 13C, 15N backbone NMR assignments of the Staphylococcus aureus small multidrug-resistance pump (Smr) in a functionally active conformation.
  Biomol NMR Assign, 4, 139-142.  
20508091 S.Seppälä, J.S.Slusky, P.Lloris-Garcerá, M.Rapp, and G.von Heijne (2010).
Control of membrane protein topology by a single C-terminal residue.
  Science, 328, 1698-1700.  
20445084 S.Sobhanifar, B.Schneider, F.Löhr, D.Gottstein, T.Ikeya, K.Mlynarczyk, W.Pulawski, U.Ghoshdastider, M.Kolinski, S.Filipek, P.Güntert, F.Bernhard, and V.Dötsch (2010).
Structural investigation of the C-terminal catalytic fragment of presenilin 1.
  Proc Natl Acad Sci U S A, 107, 9644-9649.  
19680602 S.Sobhanifar, S.Reckel, F.Junge, D.Schwarz, L.Kai, M.Karbyshev, F.Löhr, F.Bernhard, and V.Dötsch (2010).
Cell-free expression and stable isotope labelling strategies for membrane proteins.
  J Biomol NMR, 46, 33-43.  
20160448 T.A.Nguyen, S.S.Lieu, and G.Chang (2010).
An Escherichia coli-based cell-free system for large-scale production of functional mammalian membrane proteins suitable for X-ray crystallography.
  J Mol Microbiol Biotechnol, 18, 85-91.  
20861838 X.He, P.Szewczyk, A.Karyakin, M.Evin, W.X.Hong, Q.Zhang, and G.Chang (2010).
Structure of a cation-bound multidrug and toxic compound extrusion transporter.
  Nature, 467, 991-994.
PDB codes: 3mkt 3mku
19224913 B.E.Poulsen, A.Rath, and C.M.Deber (2009).
The assembly motif of a bacterial small multidrug resistance protein.
  J Biol Chem, 284, 9870-9875.  
19616329 F.Katzen, T.C.Peterson, and W.Kudlicki (2009).
Membrane protein expression: no cells required.
  Trends Biotechnol, 27, 455-460.  
19746358 K.Shimono, M.Goto, T.Kikukawa, S.Miyauchi, M.Shirouzu, N.Kamo, and S.Yokoyama (2009).
Production of functional bacteriorhodopsin by an Escherichia coli cell-free protein synthesis system supplemented with steroid detergent and lipid.
  Protein Sci, 18, 2160-2171.  
19578383 N.P.Barrera, S.C.Isaacson, M.Zhou, V.N.Bavro, A.Welch, T.A.Schaedler, M.A.Seeger, R.N.Miguel, V.M.Korkhov, H.W.van Veen, H.Venter, A.R.Walmsley, C.G.Tate, and C.V.Robinson (2009).
Mass spectrometry of membrane transporters reveals subunit stoichiometry and interactions.
  Nat Methods, 6, 585-587.  
19171975 P.D.Jeffrey (2009).
Analysis of errors in the structure determination of MsbA.
  Acta Crystallogr D Biol Crystallogr, 65, 193-199.  
19265398 S.Balaz (2009).
Modeling kinetics of subcellular disposition of chemicals.
  Chem Rev, 109, 1793-1899.  
19325113 S.G.Aller, J.Yu, A.Ward, Y.Weng, S.Chittaboina, R.Zhuo, P.M.Harrell, Y.T.Trinh, Q.Zhang, I.L.Urbatsch, and G.Chang (2009).
Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding.
  Science, 323, 1718-1722.
PDB codes: 3g5u 3g60 3g61
19536805 T.M.Blois, and J.U.Bowie (2009).
G-protein-coupled receptor structures were not built in a day.
  Protein Sci, 18, 1335-1342.  
19453273 U.A.Hellmich, and C.Glaubitz (2009).
NMR and EPR studies of membrane transporters.
  Biol Chem, 390, 815-834.  
19171974 V.M.Korkhov, and C.G.Tate (2009).
An emerging consensus for the structure of EmrE.
  Acta Crystallogr D Biol Crystallogr, 65, 186-192.  
19678712 X.Z.Li, and H.Nikaido (2009).
Efflux-mediated drug resistance in bacteria: an update.
  Drugs, 69, 1555-1623.  
18763710 D.Schwarz, V.Dötsch, and F.Bernhard (2008).
Production of membrane proteins using cell-free expression systems.
  Proteomics, 8, 3933-3946.  
18793443 J.Wu, K.A.Hassan, R.A.Skurray, and M.H.Brown (2008).
Functional analyses reveal an important role for tyrosine residues in the staphylococcal multidrug efflux protein QacA.
  BMC Microbiol, 8, 147.  
19032749 K.Charalambous, D.Miller, P.Curnow, and P.J.Booth (2008).
Lipid bilayer composition influences small multidrug transporters.
  BMC Biochem, 9, 31.  
18550820 S.Reckel, S.Sobhanifar, B.Schneider, F.Junge, D.Schwarz, F.Durst, F.Löhr, P.Güntert, F.Bernhard, and V.Dötsch (2008).
Transmembrane segment enhanced labeling as a tool for the backbone assignment of alpha-helical membrane proteins.
  Proc Natl Acad Sci U S A, 105, 8262-8267.  
18321856 Y.Elbaz, T.Salomon, and S.Schuldiner (2008).
Identification of a glycine motif required for packing in EmrE, a multidrug transporter from Escherichia coli.
  J Biol Chem, 283, 12276-12283.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.