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- EMDB-16123: Cryo-EM structure of the wild-type solitary ECF module in DDM mic... -
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Open data
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Basic information
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Title | Cryo-EM structure of the wild-type solitary ECF module in DDM micelles in the ATPase open and nucleotide-free conformation | ||||||||||||||||||
![]() | ATPase open and nucleotide-free conformation of the wild-type solitary ECF module in MSP2N2 lipid nanodiscs at 4.3 A resolution sharpened at -159 A^2. | ||||||||||||||||||
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![]() | ABC Transporter / ECF transporter complex / motor / membrane protein | ||||||||||||||||||
Function / homology | ![]() Translocases / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||||||||||||||
![]() | Thangaratnarajah C / Rheinberger J / Paulino C / Slotboom DJ | ||||||||||||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: Expulsion mechanism of the substrate-translocating subunit in ECF transporters. Authors: Chancievan Thangaratnarajah / Mark Nijland / Luís Borges-Araújo / Aike Jeucken / Jan Rheinberger / Siewert J Marrink / Paulo C T Souza / Cristina Paulino / Dirk J Slotboom / ![]() ![]() ![]() Abstract: Energy-coupling factor (ECF)-type transporters mediate the uptake of micronutrients in many bacteria. They consist of a substrate-translocating subunit (S-component) and an ATP-hydrolysing motor (ECF ...Energy-coupling factor (ECF)-type transporters mediate the uptake of micronutrients in many bacteria. They consist of a substrate-translocating subunit (S-component) and an ATP-hydrolysing motor (ECF module) Previous data indicate that the S-component topples within the membrane to alternately expose the binding site to either side of the membrane. In many ECF transporters, the substrate-free S-component can be expelled from the ECF module. Here we study this enigmatic expulsion step by cryogenic electron microscopy and reveal that ATP induces a concave-to-convex shape change of two long helices in the motor, thereby destroying the S-component's docking site and allowing for its dissociation. We show that adaptation of the membrane morphology to the conformational state of the motor may favour expulsion of the substrate-free S-component when ATP is bound and docking of the substrate-loaded S-component after hydrolysis. Our work provides a picture of bilayer-assisted chemo-mechanical coupling in the transport cycle of ECF transporters. | ||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.3 KB 23.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.6 KB | Display | ![]() |
Images | ![]() | 91 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Others | ![]() ![]() ![]() | 57.1 MB 59.3 MB 59.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 947.4 KB | Display | ![]() |
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Full document | ![]() | 947 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bmpC ![]() 8bmqC ![]() 8bmrC ![]() 8bmsC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 | ATPase open and nucleotide-free conformation of the wild-type solitary ECF module in MSP2N2 lipid nanodiscs at 4.3 A resolution sharpened at -159 A^2. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.022 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: Sharpened map obtained with DeepEMhancer used for figures.
File | emd_16123_additional_1.map | ||||||||||||
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Annotation | Sharpened map obtained with DeepEMhancer used for figures. | ||||||||||||
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Density Histograms |
-Half map: Half map 1 used during refinement and FSC...
File | emd_16123_half_map_1.map | ||||||||||||
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Annotation | Half map 1 used during refinement and FSC gold-standard resolution calculation. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 used during refinement and FSC...
File | emd_16123_half_map_2.map | ||||||||||||
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Annotation | Half map 2 used during refinement and FSC gold-standard resolution calculation. | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Wild-type solitary ECF module
Entire | Name: Wild-type solitary ECF module |
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Components |
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-Supramolecule #1: Wild-type solitary ECF module
Supramolecule | Name: Wild-type solitary ECF module / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Energy-coupling factor transporter ATP-binding protein EcfA1
Macromolecule | Name: Energy-coupling factor transporter ATP-binding protein EcfA1 type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778 |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSDNIISFDH VTFTYPDSPR PALSDLSFAI ERGSWTALIG HNGSGKSTVS KLINGLLAPD DLDKSSITVD GVKLGADTVW EVREKVGIVF QNPDNQFVGA TVSDDVAFGL ENRAVPRPEM LKIVAQAVAD VGMADYADSE PSNLSGGQKQ RVAIAGILAV KPQVIILDES ...String: GSDNIISFDH VTFTYPDSPR PALSDLSFAI ERGSWTALIG HNGSGKSTVS KLINGLLAPD DLDKSSITVD GVKLGADTVW EVREKVGIVF QNPDNQFVGA TVSDDVAFGL ENRAVPRPEM LKIVAQAVAD VGMADYADSE PSNLSGGQKQ RVAIAGILAV KPQVIILDES TSMLDPEGKE QILDLVRKIK EDNNLTVISI THDLEEAAGA DQVLVLDDGQ LLDQGKPEEI FPKVEMLKRI GLDIPFVYRL KQLLKERGIV LPDEIDDDEK LVQSLWQLNS KM UniProtKB: Energy-coupling factor transporter ATP-binding protein EcfA1 |
-Macromolecule #2: Energy-coupling factor transporter ATP-binding protein EcfA2
Macromolecule | Name: Energy-coupling factor transporter ATP-binding protein EcfA2 type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778 |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAIKFENVSY VYSPGSPLEA IGLDQLNFSL EEGKFIALVG HTGSGKSTLM QHFNALLKPT SGKIEIAGYT ITPETGNKGL KDLRRKVSLA FQFSEAQLFE NTVLKDVEYG PRNFGFSEDE AREAALKWLK KVGLKDDLIE HSPFDLSGGQ MRRVALAGVL AYEPEIICLD ...String: MAIKFENVSY VYSPGSPLEA IGLDQLNFSL EEGKFIALVG HTGSGKSTLM QHFNALLKPT SGKIEIAGYT ITPETGNKGL KDLRRKVSLA FQFSEAQLFE NTVLKDVEYG PRNFGFSEDE AREAALKWLK KVGLKDDLIE HSPFDLSGGQ MRRVALAGVL AYEPEIICLD EPAAGLDPMG RLEMMQLFKD YQAAGHTVIL VTHNMDDVAD YADDVLALEH GRLIKHASPK EVFKDSEWLQ KHHLAEPRSA RFAAKLEAAG LKLPGQPLTM PELADAIKQS LKGGEHE UniProtKB: Energy-coupling factor transporter ATP-binding protein EcfA2 |
-Macromolecule #3: Energy-coupling factor transporter transmembrane protein EcfT
Macromolecule | Name: Energy-coupling factor transporter transmembrane protein EcfT type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778 |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSKIIIGRYL PGTTFVYRVD PRAKLLTTFY FIIMIFLANN WVSYLVISIF GLAYVFATGL KARVFWDGVK PMIWMIVFTS LLQTFFMAGG KVYWHWWIFT LSSEGLINGL YVFIRFAMII LVSTVMTVTT KPLEIADAME WMLTPLKLFK VNVGMISLVI SIALRFVPTL ...String: MSKIIIGRYL PGTTFVYRVD PRAKLLTTFY FIIMIFLANN WVSYLVISIF GLAYVFATGL KARVFWDGVK PMIWMIVFTS LLQTFFMAGG KVYWHWWIFT LSSEGLINGL YVFIRFAMII LVSTVMTVTT KPLEIADAME WMLTPLKLFK VNVGMISLVI SIALRFVPTL FDQTVKIMNA QRSRGADFND GGLVKRAKSV VPMLVPLFID SLEVALDLST AMESRGYKGS EGRTRYRILE WSKVDLIPVA YCLLLTILMI TTRKH UniProtKB: Energy-coupling factor transporter transmembrane protein EcfT |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5.4 mg/mL |
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Buffer | pH: 8 / Details: 20 mM Tris, pH 8.0, 150 mM NaCl |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Details: Edwards Scancoat 6, 5 mA |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV Details: 2.9 mM fluorinated Fos-choline 8 was added prior to sample application onto grids. Grids were blotted for 3.5-4 sec.. |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-60 / Number grids imaged: 1 / Number real images: 1906 / Average exposure time: 9.0 sec. / Average electron dose: 50.1 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 1.8 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 48924 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |