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Yorodumi- PDB-8wm5: multidrug transporter EfpA from Mycobacterium tuberculosis bound ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wm5 | ||||||
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Title | multidrug transporter EfpA from Mycobacterium tuberculosis bound with lipids | ||||||
Components | Efflux pump A | ||||||
Keywords | TRANSPORT PROTEIN / multidrug transporter / EfpA / mycobacterium / lipid | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å | ||||||
Authors | Wang, S. / Liao, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structures of the Mycobacterium tuberculosis efflux pump EfpA reveal the mechanisms of transport and inhibition. Authors: Shuhui Wang / Kun Wang / Kangkang Song / Zon Weng Lai / Pengfei Li / Dongying Li / Yajie Sun / Ye Mei / Chen Xu / Maofu Liao / Abstract: As the first identified multidrug efflux pump in Mycobacterium tuberculosis (Mtb), EfpA is an essential protein and promising drug target. However, the functional and inhibitory mechanisms of EfpA ...As the first identified multidrug efflux pump in Mycobacterium tuberculosis (Mtb), EfpA is an essential protein and promising drug target. However, the functional and inhibitory mechanisms of EfpA are poorly understood. Here we report cryo-EM structures of EfpA in outward-open conformation, either bound to three endogenous lipids or the inhibitor BRD-8000.3. Three lipids inside EfpA span from the inner leaflet to the outer leaflet of the membrane. BRD-8000.3 occupies one lipid site at the level of inner membrane leaflet, competitively inhibiting lipid binding. EfpA resembles the related lysophospholipid transporter MFSD2A in both overall structure and lipid binding sites and may function as a lipid flippase. Combining AlphaFold-predicted EfpA structure, which is inward-open, we propose a complete conformational transition cycle for EfpA. Together, our results provide a structural and mechanistic foundation to comprehend EfpA function and develop EfpA-targeting anti-TB drugs. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wm5.cif.gz | 173.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wm5.ent.gz | 131.5 KB | Display | PDB format |
PDBx/mmJSON format | 8wm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wm5_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8wm5_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8wm5_validation.xml.gz | 48.6 KB | Display | |
Data in CIF | 8wm5_validation.cif.gz | 67.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/8wm5 ftp://data.pdbj.org/pub/pdb/validation_reports/wm/8wm5 | HTTPS FTP |
-Related structure data
Related structure data | 37641MC 8ufdC 8ufeC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper: (Code: givenMatrix: (-0.999999381859, 0.00107001729769, -0.000302231941025), (-0.00107097300276, -0.999994370619, 0.0031798974998), (-0.000298827694317, 0.00318021921642, 0.999994898441) ...NCS oper: (Code: given Matrix: (-0.999999381859, 0.00107001729769, -0.000302231941025), Vector: |
-Components
#1: Protein | Mass: 55620.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: H37Rv / Gene: efpA / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P9WJY5 #2: Chemical | ChemComp-PTY / #3: Chemical | ChemComp-CDL / | Has ligand of interest | Y | |
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-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: complex of multidrug efflux pump EfpA with lipids / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.11 MDa / Experimental value: NO |
Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-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: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49783 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.65 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS | Type: NCS constraints / Rms dev position: 0.103023936357 Å |