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Yorodumi- PDB-7sfq: EmrE S64V Mutant Bound to tetra(4-fluorophenyl)phosphonium at pH 8.0 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sfq | ||||||||||||
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Title | EmrE S64V Mutant Bound to tetra(4-fluorophenyl)phosphonium at pH 8.0 | ||||||||||||
Components | Multidrug transporter EmrE | ||||||||||||
Keywords | MEMBRANE PROTEIN / Multidrug resistance protein / SMR Transporter / Efflux protein / Proton-coupled | ||||||||||||
Function / homology | Function and homology information EmrE multidrug transporter complex / choline transmembrane transporter activity / glycine betaine transport / amino-acid betaine transmembrane transporter activity / choline transport / xenobiotic detoxification by transmembrane export across the plasma membrane / xenobiotic transport / antiporter activity / response to osmotic stress / xenobiotic transmembrane transporter activity ...EmrE multidrug transporter complex / choline transmembrane transporter activity / glycine betaine transport / amino-acid betaine transmembrane transporter activity / choline transport / xenobiotic detoxification by transmembrane export across the plasma membrane / xenobiotic transport / antiporter activity / response to osmotic stress / xenobiotic transmembrane transporter activity / transmembrane transporter activity / xenobiotic metabolic process / transmembrane transport / cellular response to xenobiotic stimulus / response to xenobiotic stimulus / DNA damage response / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | SOLID-STATE NMR / molecular dynamics | ||||||||||||
Authors | Shcherbakov, A.A. / Spreacker, P.J. / Dregni, A.J. / Henzler-Wildman, K.A. / Hong, M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2022 Title: High-pH structure of EmrE reveals the mechanism of proton-coupled substrate transport. Authors: Shcherbakov, A.A. / Spreacker, P.J. / Dregni, A.J. / Henzler-Wildman, K.A. / Hong, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sfq.cif.gz | 623.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sfq.ent.gz | 528.7 KB | Display | PDB format |
PDBx/mmJSON format | 7sfq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sfq_validation.pdf.gz | 497.4 KB | Display | wwPDB validaton report |
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Full document | 7sfq_full_validation.pdf.gz | 587.9 KB | Display | |
Data in XML | 7sfq_validation.xml.gz | 35 KB | Display | |
Data in CIF | 7sfq_validation.cif.gz | 52 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sf/7sfq ftp://data.pdbj.org/pub/pdb/validation_reports/sf/7sfq | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11975.331 Da / Num. of mol.: 2 / Mutation: S64V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: emrE / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P23895 #2: Chemical | ChemComp-VCJ / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: SOLID-STATE NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: liposome Contents: 0.27 mg/uL [U-13C; U-15N; U-2H] Multidrug Resistance Protein E (EmrE), Complex with tetra(4-fluorophenyl)phosphonium, 9.5 ug/uL F4TPP, 0.44 mg/uL [U-99% 2H] d54-DMPC, bilayers Details: Uniformly C,D,N-labelled S64V EmrE, with F4-TPP in d54-DMPC bilayers at 1:25 P:L ratio at pH 8.0 Label: Sample_1 / Solvent system: bilayers | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.07 M / Label: Conditions_1 / pH: 8 / PH err: 0.1 / Pressure: 1 atm / Temperature: 285 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 2 Details: The authors state that the starting model for structure calculation was 7JK8. The ligand VCJ was removed from the 7JK8 structure and re-docked using HADDOCK, under new constraints measured ...Details: The authors state that the starting model for structure calculation was 7JK8. The ligand VCJ was removed from the 7JK8 structure and re-docked using HADDOCK, under new constraints measured in the present study. The docked structures best agreeing with experiment were further refined by all-atom MD simulations in explicit lipid bilayers to generate the ensemble deposited for this study. | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 82 / Conformers submitted total number: 10 |