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Yorodumi- PDB-8bmr: Cryo-EM structure of the wild-type solitary ECF module in MSP2N2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bmr | ||||||||||||||||||
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Title | Cryo-EM structure of the wild-type solitary ECF module in MSP2N2 lipid nanodiscs in the ATPase open and nucleotide-free conformation | ||||||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / ABC Transporter / ECF transporter complex / motor | ||||||||||||||||||
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 / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002 (bacteria) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||||||||
Authors | Thangaratnarajah, C. / Rheinberger, J. / Paulino, C. / Slotboom, D.J. | ||||||||||||||||||
Funding support | European Union, Netherlands, 5items
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Citation | Journal: Nat Commun / Year: 2023 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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bmr.cif.gz | 150.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bmr.ent.gz | 117.2 KB | Display | PDB format |
PDBx/mmJSON format | 8bmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/8bmr ftp://data.pdbj.org/pub/pdb/validation_reports/bm/8bmr | HTTPS FTP |
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-Related structure data
Related structure data | 16122MC 8bmpC 8bmqC 8bmsC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 30801.861 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002 (bacteria) Strain: ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14 Gene: ecfA1, cbiO1, Ldb0424 / Plasmid: p2BAD / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: Q1GBJ0, Translocases |
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#2: Protein | Mass: 31672.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002 (bacteria) Strain: ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778 Gene: ecfA2, cbiO2, Ldb0425 / Plasmid: p2BAD / Production host: Escherichia coli MC1061 (bacteria) References: UniProt: Q1GBI9, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances |
#3: Protein | Mass: 30290.283 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002 (bacteria) Strain: ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778 Gene: cbiQ, ecfT, Ldb0426 / Plasmid: p2BAD / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: Q1GBI8 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Wild-type solitary ECF module / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002 (bacteria) |
Source (recombinant) | Organism: Escherichia coli MC1061 (bacteria) / Plasmid: p2BAD |
Buffer solution | pH: 8 / Details: 20 mM Tris, pH 8.0, 150 mM NaCl |
Specimen | Conc.: 5.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: Edwards Scancoat 6, 5 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 288 K Details: 2.9 mM fluorinated Fos-choline 8 was added prior to sample application onto grids. Grids were blotted for 3.5-4 sec. |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Calibrated magnification: 48924 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 1800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 9 sec. / Electron dose: 50.1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 12071 Details: Dataset 1: 2200 movies Dataset 2: 4608 movie Dataset 3: 2101 movie Dataset 4: 3162 movie |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 60 / Used frames/image: 1-60 |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2889054 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93755 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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