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Yorodumi- PDB-8fhk: Heterodimeric ABC transporter BmrCD in the occluded conformation ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fhk | ||||||
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Title | Heterodimeric ABC transporter BmrCD in the occluded conformation bound to ATP: BmrCD_OC-ATP | ||||||
Components |
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Keywords | TRANSLOCASE / transporter / complex / lipids / MEMBRANE 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 / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / response to antibiotic / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Tang, Q. / Mchaourab, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter. Authors: Qingyu Tang / Matt Sinclair / Hale S Hasdemir / Richard A Stein / Erkan Karakas / Emad Tajkhorshid / Hassane S Mchaourab / Abstract: Here we used cryo-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy (DEER), and molecular dynamics (MD) simulations, to capture and characterize ATP- and substrate-bound ...Here we used cryo-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy (DEER), and molecular dynamics (MD) simulations, to capture and characterize ATP- and substrate-bound inward-facing (IF) and occluded (OC) conformational states of the heterodimeric ATP binding cassette (ABC) multidrug exporter BmrCD in lipid nanodiscs. Supported by DEER analysis, the structures reveal that ATP-powered isomerization entails changes in the relative symmetry of the BmrC and BmrD subunits that propagates from the transmembrane domain to the nucleotide binding domain. The structures uncover asymmetric substrate and Mg binding which we hypothesize are required for triggering ATP hydrolysis preferentially in one of the nucleotide-binding sites. MD simulations demonstrate that multiple lipid molecules differentially bind the IF versus the OC conformation thus establishing that lipid interactions modulate BmrCD energy landscape. Our findings are framed in a model that highlights the role of asymmetric conformations in the ATP-coupled transport with general implications to the mechanism of ABC transporters. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fhk.cif.gz | 435.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fhk.ent.gz | 357.2 KB | Display | PDB format |
PDBx/mmJSON format | 8fhk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fhk_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8fhk_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8fhk_validation.xml.gz | 43.9 KB | Display | |
Data in CIF | 8fhk_validation.cif.gz | 63 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/8fhk ftp://data.pdbj.org/pub/pdb/validation_reports/fh/8fhk | HTTPS FTP |
-Related structure data
Related structure data | 29087MC 8fmvC 8fpfC 8szcC 8t1pC 8t3kC 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: 77369.898 Da / Num. of mol.: 1 / Mutation: C154A,C256A,C351A,E592Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: yheH, BSU09720 / Production host: Escherichia coli (E. coli) References: UniProt: O07549, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate | ||||||
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#2: Protein | Mass: 67602.961 Da / Num. of mol.: 1 / Mutation: D500Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: yheI, BSU09710 / Production host: Escherichia coli (E. coli) References: UniProt: O07550, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate | ||||||
#3: Chemical | #4: Chemical | ChemComp-POV / ( #5: Chemical | Has ligand of interest | Y | |
-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: Heterodimeric BmrCD with ligands ATP and lipids / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 15 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91128 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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