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Yorodumi- EMDB-13095: CryoEM structure of the ABC transporter BmrA E504A mutant in comp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13095 | |||||||||||||||||||||
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Title | CryoEM structure of the ABC transporter BmrA E504A mutant in complex with ATP-Mg | |||||||||||||||||||||
Map data | Sharpened map | |||||||||||||||||||||
Sample |
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Keywords | BmrA ABC transporter complex with ATP-Mg multidrug resistance / TRANSPORT PROTEIN | |||||||||||||||||||||
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 / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Bacillus subtilis (bacteria) / Bacillus subtilis (strain 168) (bacteria) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||||||||
Authors | Gobet A / Schoehn G | |||||||||||||||||||||
Funding support | France, 6 items
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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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13095.map.gz | 59.8 MB | EMDB map data format | |
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Header (meta data) | emd-13095-v30.xml emd-13095.xml | 23.2 KB 23.2 KB | Display Display | EMDB header |
Images | emd_13095.png | 72.1 KB | ||
Filedesc metadata | emd-13095.cif.gz | 6.6 KB | ||
Others | emd_13095_additional_1.map.gz emd_13095_half_map_1.map.gz emd_13095_half_map_2.map.gz | 31.5 MB 59.4 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13095 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13095 | HTTPS FTP |
-Validation report
Summary document | emd_13095_validation.pdf.gz | 757.3 KB | Display | EMDB validaton report |
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Full document | emd_13095_full_validation.pdf.gz | 756.9 KB | Display | |
Data in XML | emd_13095_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_13095_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13095 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13095 | HTTPS FTP |
-Related structure data
Related structure data | 7ow8MC 4749C 6r72C 6r81C 7bg4C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13095.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.052 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unsharpened map
File | emd_13095_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: even half map, unsharpened
File | emd_13095_half_map_1.map | ||||||||||||
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Annotation | even half map, unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: odd half map, unsharpened
File | emd_13095_half_map_2.map | ||||||||||||
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Annotation | odd half map, unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of BmrA with ATP-Mg
Entire | Name: Complex of BmrA with ATP-Mg |
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Components |
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-Supramolecule #1: Complex of BmrA with ATP-Mg
Supramolecule | Name: Complex of BmrA with ATP-Mg / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Bacillus subtilis (bacteria) / Strain: 168 |
Molecular weight | Theoretical: 130 KDa |
-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: Bacillus subtilis (strain 168) (bacteria) / Strain: 168 |
Molecular weight | Theoretical: 65.489824 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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 LEN 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 4400 / Average exposure time: 5.0 sec. / Average electron dose: 37.95 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |