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- EMDB-12483: Cryo-EM structure of the folate-specific ECF transporter complex ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12483 | |||||||||||||||
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Title | Cryo-EM structure of the folate-specific ECF transporter complex in DDM micelles | |||||||||||||||
![]() | Inward-facing apo conformation of the folate-specific ECF transporter complex in DDM micelles at 3.4 A resolution sharpened at -62 A^2. | |||||||||||||||
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![]() | ABC Transporter / Type III ABC Transporter / ECF transporter complex / Folate transporter / Membrane protein / TRANSPORT 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 / membrane / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||
![]() | Thangaratnarajah C / Rheinberger J | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Insights into the bilayer-mediated toppling mechanism of a folate-specific ECF transporter by cryo-EM. Authors: Chancievan Thangaratnarajah / Jan Rheinberger / Cristina Paulino / Dirk J Slotboom / ![]() Abstract: Energy-coupling factor (ECF)-type transporters are small, asymmetric membrane protein complexes (∼115 kDa) that consist of a membrane-embedded, substrate-binding protein (S component) and a ...Energy-coupling factor (ECF)-type transporters are small, asymmetric membrane protein complexes (∼115 kDa) that consist of a membrane-embedded, substrate-binding protein (S component) and a tripartite ATP-hydrolyzing module (ECF module). They import micronutrients into bacterial cells and have been proposed to use a highly unusual transport mechanism, in which the substrate is dragged across the membrane by a toppling motion of the S component. However, it remains unclear how the lipid bilayer could accommodate such a movement. Here, we used cryogenic electron microscopy at 200 kV to determine structures of a folate-specific ECF transporter in lipid nanodiscs and detergent micelles at 2.7- and 3.4-Å resolution, respectively. The structures reveal an irregularly shaped bilayer environment around the membrane-embedded complex and suggest that toppling of the S component is facilitated by protein-induced membrane deformations. In this way, structural remodeling of the lipid bilayer environment is exploited to guide the transport process. | |||||||||||||||
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 | ![]() | 59.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27 KB 27 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.2 KB | Display | ![]() |
Images | ![]() | 158.6 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 7.3 KB | ||
Others | ![]() ![]() ![]() | 49.3 MB 49.6 MB 49.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nntMC ![]() 7nnuC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data size: 141.7 Data #1: Unaligned movie frames of ECF-FolT2 in DDM micelles (Dataset 1, Quantifoil grid) [micrographs - multiframe] Data #2: Unaligned movie frames of ECF-FolT2 in DDM micelles (Dataset 2, UltrAuFoil grid) [micrographs - multiframe]) |
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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 | Inward-facing apo conformation of the folate-specific ECF transporter complex in DDM micelles at 3.4 A resolution sharpened at -62 A^2. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.012 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Sharpened map obtained with LocalDeblur used for model...
File | emd_12483_additional_1.map | ||||||||||||
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Annotation | Sharpened map obtained with LocalDeblur used for model building and figures. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 used during refinement and FSC...
File | emd_12483_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_12483_half_map_2.map | ||||||||||||
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Annotation | Half map 2 used during refinement and FSC gold-standard resolution calculation. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Folate-specific ECF transporter complex
Entire | Name: Folate-specific ECF transporter complex |
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Components |
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-Supramolecule #1: Folate-specific ECF transporter complex
Supramolecule | Name: Folate-specific ECF transporter complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() Strain: ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778 |
-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 / Number of copies: 1 / Enantiomer: LEVO / EC number: Translocases |
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Source (natural) | Organism: ![]() Strain: ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778 |
Molecular weight | Theoretical: 33.166418 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MHHHHHHHHH HGENLYFQGS DNIISFDHVT FTYPDSPRPA LSDLSFAIER GSWTALIGHN GSGKSTVSKL INGLLAPDDL DKSSITVDG VKLGADTVWE VREKVGIVFQ NPDNQFVGAT VSDDVAFGLE NRAVPRPEML KIVAQAVADV GMADYADSEP S NLSGGQKQ ...String: MHHHHHHHHH HGENLYFQGS DNIISFDHVT FTYPDSPRPA LSDLSFAIER GSWTALIGHN GSGKSTVSKL INGLLAPDDL DKSSITVDG VKLGADTVWE VREKVGIVFQ NPDNQFVGAT VSDDVAFGLE NRAVPRPEML KIVAQAVADV GMADYADSEP S NLSGGQKQ RVAIAGILAV KPQVIILDES TSMLDPEGKE QILDLVRKIK EDNNLTVISI THDLEEAAGA DQVLVLDDGQ LL DQGKPEE IFPKVEMLKR IGLDIPFVYR LKQLLKERGI VLPDEIDDDE KLVQSLWQLN SKM 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 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances |
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Source (natural) | Organism: ![]() Strain: ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778 |
Molecular weight | Theoretical: 31.672156 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAIKFENVSY VYSPGSPLEA IGLDQLNFSL EEGKFIALVG HTGSGKSTLM QHFNALLKPT SGKIEIAGYT ITPETGNKGL KDLRRKVSL AFQFSEAQLF ENTVLKDVEY GPRNFGFSED EAREAALKWL KKVGLKDDLI EHSPFDLSGG QMRRVALAGV L AYEPEIIC ...String: MAIKFENVSY VYSPGSPLEA IGLDQLNFSL EEGKFIALVG HTGSGKSTLM QHFNALLKPT SGKIEIAGYT ITPETGNKGL KDLRRKVSL AFQFSEAQLF ENTVLKDVEY GPRNFGFSED EAREAALKWL KKVGLKDDLI EHSPFDLSGG QMRRVALAGV L AYEPEIIC LDEPAAGLDP MGRLEMMQLF KDYQAAGHTV ILVTHNMDDV ADYADDVLAL EHGRLIKHAS PKEVFKDSEW LQ KHHLAEP RSARFAAKLE AAGLKLPGQP LTMPELADAI KQSLKGGEHE UniProtKB: Energy-coupling factor transporter ATP-binding protein EcfA2 |
-Macromolecule #3: Folate family ECF transporter S component
Macromolecule | Name: Folate family ECF transporter S component / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778 |
Molecular weight | Theoretical: 20.483604 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKSESKVSSK LELRELVLLA MVIAIKVILG QFKVGNATLQ VGLGFIGSVM LGYLFGPWWG FAGGALSDLV SSVIFGNLGG FFIGFTLTA ALGPMIYGFF LYKQPIQIWR VIASVICVTV ICNIGLNTLW VSMMYGINFM VALSSRILKE MITPWIQMVA V WFILEGLS RVKLSRKFWS HPQFEK UniProtKB: Conserved hypothetical membrane protein |
-Macromolecule #4: Energy-coupling factor transporter transmembrane protein EcfT
Macromolecule | Name: Energy-coupling factor transporter transmembrane protein EcfT type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778 |
Molecular weight | Theoretical: 30.290283 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSKIIIGRYL PGTTFVYRVD PRAKLLTTFY FIIMIFLANN WVSYLVISIF GLAYVFATGL KARVFWDGVK PMIWMIVFTS LLQTFFMAG GKVYWHWWIF TLSSEGLING LYVFIRFAMI ILVSTVMTVT TKPLEIADAM EWMLTPLKLF KVNVGMISLV I SIALRFVP ...String: MSKIIIGRYL PGTTFVYRVD PRAKLLTTFY FIIMIFLANN WVSYLVISIF GLAYVFATGL KARVFWDGVK PMIWMIVFTS LLQTFFMAG GKVYWHWWIF TLSSEGLING LYVFIRFAMI ILVSTVMTVT TKPLEIADAM EWMLTPLKLF KVNVGMISLV I SIALRFVP TLFDQTVKIM NAQRSRGADF NDGGLVKRAK SVVPMLVPLF IDSLEVALDL STAMESRGYK GSEGRTRYRI LE WSKVDLI PVAYCLLLTI LMITTRKH 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 | 7.9 mg/mL |
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Buffer | pH: 8 Details: 20 mM Tris, pH 8.0, 150 mM NaCl, 0.0261 % (w/v) DDM |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: 5 mA; for dataset 2. |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV Details: Grid was blotted for 4 sec after a wait time for 2.5 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: 2 / Number real images: 823 / Average exposure time: 9.0 sec. / Average electron dose: 53.3 e/Å2 Details: Dataset 1: 466 movies (Quantifoil grid) Dataset 2: 357 movies (UltrAuFoil grid) |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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 |
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Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL | ||||||||||
Output model | ![]() PDB-7nnt: |