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Yorodumi- PDB-6r72: Crystal structure of BmrA-E504A in an outward-facing conformation -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r72 | ||||||||||||
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Title | Crystal structure of BmrA-E504A in an outward-facing conformation | ||||||||||||
Components | Multidrug exporter ATP-binding cassette | ||||||||||||
Keywords | TRANSPORT PROTEIN / ABC transporter BmrA Multi-drug transporter | ||||||||||||
Function / homology | Function and homology information ATPase-coupled lipid transmembrane transporter activity / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / ABC-type transporter activity / transmembrane transport / response to antibiotic / ATP hydrolysis activity / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Bacillus subtilis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.95 Å | ||||||||||||
Authors | Chaptal, V. / Zampieri, V. / Kilburg, A. / Magnard, S. / Falson, P. | ||||||||||||
Funding support | France, 3items
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Citation | Journal: Sci Adv / Year: 2022 Title: Substrate-bound and substrate-free outward-facing structures of a multidrug ABC exporter. Authors: Vincent Chaptal / Veronica Zampieri / Benjamin Wiseman / Cédric Orelle / Juliette Martin / Kim-Anh Nguyen / Alexia Gobet / Margot Di Cesare / Sandrine Magnard / Waqas Javed / Jad Eid / ...Authors: Vincent Chaptal / Veronica Zampieri / Benjamin Wiseman / Cédric Orelle / Juliette Martin / Kim-Anh Nguyen / Alexia Gobet / Margot Di Cesare / Sandrine Magnard / Waqas Javed / Jad Eid / Arnaud Kilburg / Marine Peuchmaur / Julien Marcoux / Luca Monticelli / Martin Hogbom / Guy Schoehn / Jean-Michel Jault / Ahcène Boumendjel / Pierre Falson / Abstract: Multidrug ABC transporters translocate drugs across membranes by a mechanism for which the molecular features of drug release are so far unknown. Here, we resolved three ATP-Mg-bound outward-facing ...Multidrug ABC transporters translocate drugs across membranes by a mechanism for which the molecular features of drug release are so far unknown. Here, we resolved three ATP-Mg-bound outward-facing conformations of the (homodimeric) BmrA by x-ray crystallography and single-particle cryo-electron microscopy (EM) in detergent solution, one of them with rhodamine 6G (R6G), a substrate exported by BmrA when overexpressed in . Two R6G molecules bind to the drug-binding cavity at the level of the outer leaflet, between transmembrane (TM) helices 1-2 of one monomer and TM5'-6' of the other. They induce a rearrangement of TM1-2, highlighting a local flexibility that we confirmed by hydrogen/deuterium exchange and molecular dynamics simulations. In the absence of R6G, simulations show a fast postrelease occlusion of the cavity driven by hydrophobicity, while when present, R6G can move within the cavity, maintaining it open. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r72.cif.gz | 901 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r72.ent.gz | 749.6 KB | Display | PDB format |
PDBx/mmJSON format | 6r72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r7/6r72 ftp://data.pdbj.org/pub/pdb/validation_reports/r7/6r72 | HTTPS FTP |
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-Related structure data
Related structure data | 4749C 6r81C 7bg4C 7ow8C 2hydS 3b60S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 65747.141 Da / Num. of mol.: 4 / Mutation: E504A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_3307 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Variant (production host): C43, Delate-AcrB / References: UniProt: A0A164TVX9, UniProt: O06967*PLUS #2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-MG / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 68.5 % / Description: rods |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 23-27% PEG 1000, 0.1M Tris pH 8.5 / PH range: 8-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.92→80.6 Å / Num. obs: 20484 / % possible obs: 92 % / Observed criterion σ(F): 1.25 / Redundancy: 3.5 % / Biso Wilson estimate: 178.75 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.65 |
Reflection shell | Resolution: 3.92→4.3 Å / Rmerge(I) obs: 3.7 / Mean I/σ(I) obs: 1.39 / Num. unique obs: 959 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3b60, 2hyd Resolution: 3.95→28.42 Å / Cor.coef. Fo:Fc: 0.708 / Cor.coef. Fo:Fc free: 0.644 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 1.354 Details: 9 big cycles of 500 small cycles each. Refinement R values go up in the first cycles before going down and converging to a stable value in the later stages. Use of TLS refinement. Use of ...Details: 9 big cycles of 500 small cycles each. Refinement R values go up in the first cycles before going down and converging to a stable value in the later stages. Use of TLS refinement. Use of NCS, strong initially, only loosened in the last stages of refinement Data displaying very strong anisotropy.
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Displacement parameters | Biso mean: 113.9 Å2
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Refine analyze | Luzzati coordinate error obs: 0.79 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.95→28.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.95→4.17 Å / Total num. of bins used: 50
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Refinement TLS params. | T12: -0.1432 Å2 / T23: -0.1603 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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