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- EMDB-12170: Multidrug resistance transporter BmrA mutant E504A bound with ATP... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12170 | ||||||||||||
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Title | Multidrug resistance transporter BmrA mutant E504A bound with ATP, Mg, and Rhodamine 6G solved by Cryo-EM | ||||||||||||
![]() | Main map used for model building. | ||||||||||||
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![]() | membrane protein / ABC transporter / multidrug resistance / TRANSPORT PROTEIN | ||||||||||||
Function / homology | ![]() 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 / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||||||||
![]() | Wiseman B / Chaptal V | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.6 KB 17.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.9 KB | Display | ![]() |
Images | ![]() | 51 KB | ||
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() | 24.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bg4MC ![]() 4749C ![]() 6r72C ![]() 6r81C ![]() 7ow8C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Main map used for model building. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Sharpened map used to aid and improve model building in many areas
File | emd_12170_additional_1.map | ||||||||||||
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Annotation | Sharpened map used to aid and improve model building in many areas | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Multidrug resistance transporter from Bacillus subtilis bound wit...
Entire | Name: Multidrug resistance transporter from Bacillus subtilis bound with ATP, Mg, and Rhodamine 6G. |
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Components |
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-Supramolecule #1: Multidrug resistance transporter from Bacillus subtilis bound wit...
Supramolecule | Name: Multidrug resistance transporter from Bacillus subtilis bound with ATP, Mg, and Rhodamine 6G. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: mutant E504A |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Multidrug resistance ABC transporter ATP-binding/permease protein BmrA
Macromolecule | Name: Multidrug resistance ABC transporter ATP-binding/permease protein BmrA type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO EC number: Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 65.747141 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSSSHHHHHH MPTKKQKSKS KLKPFFALVR RTNPSYGKLA FALALSVVTT LVSLLIPLLT KQLVDGFSMS NLSGTQIGLI ALVFFVQAG LSAYATYALN YNGQKIISGL RELLWKKLIK LPVSYFDTNA SGETVSRVTN DTMVVKELIT THISGFITGI I SVIGSLTI ...String: MSSSHHHHHH MPTKKQKSKS KLKPFFALVR RTNPSYGKLA FALALSVVTT LVSLLIPLLT KQLVDGFSMS NLSGTQIGLI ALVFFVQAG LSAYATYALN YNGQKIISGL RELLWKKLIK LPVSYFDTNA SGETVSRVTN DTMVVKELIT THISGFITGI I SVIGSLTI LFIMNWKLTL LVLVVVPLAA LILVPIGRKM FSISRETQDE TARFTGLLNQ ILPEIRLVKA SNAEDVEYGR GK MGISSLF KLGVREAKVQ SLVGPLISLV LMAALVAVIG YGGMQVSSGE LTAGALVAFI LYLFQIIMPM GQITTFFTQL QKS IGATER MIEILAEEEE DTVTGKQIEN AHLPIQLDRV SFGYKPDQLI LKEVSAVIEA GKVTAIVGPS GGGKTTLFKL LERF YSPTA GTIRLGDEPV DTYSLESWRE HIGYVSQESP LMSGTIRENI CYGLERDVTD AEIEKAAEMA YALNFIKELP NQFDT EVGE RGIMLSGGQR QRIAIARALL RNPSILMLDA ATSSLDSQSE KSVQQALEVL MEGRTTIVIA HRLSTVVDAD QLLFVE KGE ITGRGTHHEL MASHGLYRDF AEQQLKMNAD LENKAG UniProtKB: Multidrug resistance ABC transporter ATP-binding/permease protein BmrA |
-Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: RHODAMINE 6G
Macromolecule | Name: RHODAMINE 6G / type: ligand / ID: 4 / Number of copies: 2 / Formula: RHQ |
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Molecular weight | Theoretical: 443.557 Da |
Chemical component information | ![]() ChemComp-R6G: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3.5 mg/mL |
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Buffer | pH: 8 |
Grid | Model: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3477 / Average exposure time: 5.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 187 |
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Output model | ![]() PDB-7bg4: |