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Yorodumi- EMDB-12484: Cryo-EM structure of the folate-specific ECF transporter complex ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12484 | |||||||||||||||
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Title | Cryo-EM structure of the folate-specific ECF transporter complex in MSP2N2 lipid nanodiscs | |||||||||||||||
Map data | Inward-facing apo conformation of the folate-specific ECF transporter complex in MSP2N2 lipid nanodiscs at 2.7 A resolution sharpened at -44 A^2. | |||||||||||||||
Sample |
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Keywords | ABC Transporter / Type III ABC Transporter / ECF transporter complex / Folate transporter / Membrane protein / TRANSPORT PROTEIN | |||||||||||||||
Function / homology | Function and homology information 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 | Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778) (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||||||||
Authors | Thangaratnarajah C / Rheinberger J | |||||||||||||||
Funding support | Netherlands, 4 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12484.map.gz | 202.5 MB | EMDB map data format | |
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Header (meta data) | emd-12484-v30.xml emd-12484.xml | 27.6 KB 27.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12484_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_12484.png | 149.5 KB | ||
Masks | emd_12484_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-12484.cif.gz | 7.4 KB | ||
Others | emd_12484_additional_1.map.gz emd_12484_half_map_1.map.gz emd_12484_half_map_2.map.gz | 171.3 MB 172 MB 172 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12484 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12484 | HTTPS FTP |
-Validation report
Summary document | emd_12484_validation.pdf.gz | 962.3 KB | Display | EMDB validaton report |
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Full document | emd_12484_full_validation.pdf.gz | 961.9 KB | Display | |
Data in XML | emd_12484_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | emd_12484_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12484 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12484 | HTTPS FTP |
-Related structure data
Related structure data | 7nnuMC 7nntC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10942 (Title: Cryo-EM structure of the folate-specific ECF transporter complex in MSP2N2 lipid nanodiscs (200 kV) Data size: 1.1 TB Data #1: Unaligned movie frames of ECF-FolT2 in MSP2N2 lipid nanodiscs (Dataset 1) [micrographs - multiframe] Data #2: Unaligned movie frames of ECF-FolT2 in MSP2N2 lipid nanodiscs (Dataset 2) [micrographs - multiframe] Data #3: Unaligned movie frames of ECF-FolT2 in MSP2N2 lipid nanodiscs (Dataset 3) [micrographs - multiframe] Data #4: Unaligned movie frames of ECF-FolT2 in MSP2N2 lipid nanodiscs (Dataset 3) [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12484.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Inward-facing apo conformation of the folate-specific ECF transporter complex in MSP2N2 lipid nanodiscs at 2.7 A resolution sharpened at -44 A^2. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.771 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12484_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Sharpened map obtained with LocalDeblur used for model...
File | emd_12484_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_12484_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_12484_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 |
-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: #1-#4 |
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Source (natural) | Organism: Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778) (bacteria) 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: Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778) (bacteria) Strain: ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778 |
Molecular weight | Theoretical: 33.166418 KDa |
Recombinant expression | Organism: Escherichia coli MC1061 (bacteria) |
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: Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778) (bacteria) Strain: ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778 |
Molecular weight | Theoretical: 31.672156 KDa |
Recombinant expression | Organism: Escherichia coli MC1061 (bacteria) |
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: Conserved hypothetical membrane protein
Macromolecule | Name: Conserved hypothetical membrane protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778) (bacteria) Strain: ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778 |
Molecular weight | Theoretical: 20.483604 KDa |
Recombinant expression | Organism: Escherichia coli MC1061 (bacteria) |
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: Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778) (bacteria) Strain: ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778 |
Molecular weight | Theoretical: 30.290283 KDa |
Recombinant expression | Organism: Escherichia coli MC1061 (bacteria) |
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 |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 35 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 7.9 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 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 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 3-4 sec.. |
-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: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Frames/image: 1-60 / Number grids imaged: 3 / Number real images: 4722 / Average exposure time: 9.0 sec. / Average electron dose: 51.1 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL | ||||||||||
Output model | PDB-7nnu: |