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Yorodumi- PDB-6jbh: Cryo-EM structure and transport mechanism of a wall teichoic acid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jbh | ||||||
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Title | Cryo-EM structure and transport mechanism of a wall teichoic acid ABC transporter | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / ABC Transporter | ||||||
Biological species | Alicyclobacillus herbarius (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.94 Å | ||||||
Authors | Chen, L. / Hou, W.T. / Fan, T. / Li, Y.H. / Liu, B.H. / Jiang, Y.L. / Sun, L.F. / Chen, Y. / Zhou, C.Z. | ||||||
Funding support | China, 1items
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Citation | Journal: mBio / Year: 2020 Title: Cryo-electron Microscopy Structure and Transport Mechanism of a Wall Teichoic Acid ABC Transporter. Authors: Li Chen / Wen-Tao Hou / Tao Fan / Banghui Liu / Ting Pan / Yu-Hui Li / Yong-Liang Jiang / Wen Wen / Zhi-Peng Chen / Linfeng Sun / Cong-Zhao Zhou / Yuxing Chen / Abstract: The wall teichoic acid (WTA) is a major cell wall component of Gram-positive bacteria, such as methicillin-resistant (MRSA), a common cause of fatal clinical infections in humans. Thus, the ...The wall teichoic acid (WTA) is a major cell wall component of Gram-positive bacteria, such as methicillin-resistant (MRSA), a common cause of fatal clinical infections in humans. Thus, the indispensable ABC transporter TarGH, which flips WTA from cytoplasm to extracellular space, becomes a promising target of anti-MRSA drugs. Here, we report the 3.9-Å cryo-electron microscopy (cryo-EM) structure of a 50% sequence-identical homolog of TarGH from at an ATP-free and inward-facing conformation. Structural analysis combined with activity assays enables us to clearly decode the binding site and inhibitory mechanism of the anti-MRSA inhibitor Targocil, which targets TarGH. Moreover, we propose a "crankshaft conrod" mechanism utilized by TarGH, which can be applied to similar ABC transporters that translocate a rather big substrate through relatively subtle conformational changes. These findings provide a structural basis for the rational design and optimization of antibiotics against MRSA. The wall teichoic acid (WTA) is a major component of cell wall and a pathogenic factor in methicillin-resistant (MRSA). The ABC transporter TarGH is indispensable for flipping WTA precursor from cytoplasm to the extracellular space, thus making it a promising drug target for anti-MRSA agents. The 3.9-Å cryo-EM structure of a TarGH homolog helps us to decode the binding site and inhibitory mechanism of a recently reported inhibitor, Targocil, and provides a structural platform for rational design and optimization of potential antibiotics. Moreover, we propose a "crankshaft conrod" mechanism to explain how a big substrate is translocated through subtle conformational changes of type II exporters. These findings advance our understanding of anti-MRSA drug design and ABC transporters. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6jbh.cif.gz | 193.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jbh.ent.gz | 156.5 KB | Display | PDB format |
PDBx/mmJSON format | 6jbh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jbh_validation.pdf.gz | 950.2 KB | Display | wwPDB validaton report |
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Full document | 6jbh_full_validation.pdf.gz | 960 KB | Display | |
Data in XML | 6jbh_validation.xml.gz | 33 KB | Display | |
Data in CIF | 6jbh_validation.cif.gz | 47.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/6jbh ftp://data.pdbj.org/pub/pdb/validation_reports/jb/6jbh | HTTPS FTP |
-Related structure data
Related structure data | 9790MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 30201.881 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alicyclobacillus herbarius (bacteria) / Production host: Escherichia coli (E. coli) #2: Protein | Mass: 33066.285 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alicyclobacillus herbarius (bacteria) / Production host: Escherichia coli (E. coli) Sequence details | Sequences of TarG has deposited to NCBI with accession ID WP_026962790.1, and N-terminal ...Sequences of TarG has deposited to NCBI with accession ID WP_026962790.1, and N-terminal MGHHHHHHHH | |
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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: wall teichoic acid ABC transporter TarGH / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Alicyclobacillus herbarius (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 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 |
Image recording | Electron dose: 64 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3228: / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95416 / Symmetry type: POINT |
Atomic model building | B value: 198.567 / Protocol: AB INITIO MODEL |