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- EMDB-9790: Cryo-EM structure and transport mechanism of a wall teichoic acid... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9790 | |||||||||
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Title | Cryo-EM structure and transport mechanism of a wall teichoic acid ABC transporter | |||||||||
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![]() | ABC Transporter / TRANSPORT PROTEIN | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.94 Å | |||||||||
![]() | Chen L / Hou WT | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 28.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.2 KB 11.2 KB | Display Display | ![]() |
Images | ![]() | 61 KB | ||
Filedesc metadata | ![]() | 5.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jbhMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : wall teichoic acid ABC transporter TarGH
Entire | Name: wall teichoic acid ABC transporter TarGH |
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Components |
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-Supramolecule #1: wall teichoic acid ABC transporter TarGH
Supramolecule | Name: wall teichoic acid ABC transporter TarGH / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: TarH
Macromolecule | Name: TarH / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 30.201881 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MEHAVIVENV TKKYKLFKRT SERLLDMILP GGYGEDFYAL RNVSFTADKG DVIGIVGVNG SGKSTLSNII AGILPPTSGT IKIDGQASL IAISSGLNNQ LTGRENIELK CLMLGFSKKQ IRAMEPDIIE FADIGKFIDQ PVKTYSSGMK SRLGFAISVN I DPDVLVID ...String: MEHAVIVENV TKKYKLFKRT SERLLDMILP GGYGEDFYAL RNVSFTADKG DVIGIVGVNG SGKSTLSNII AGILPPTSGT IKIDGQASL IAISSGLNNQ LTGRENIELK CLMLGFSKKQ IRAMEPDIIE FADIGKFIDQ PVKTYSSGMK SRLGFAISVN I DPDVLVID EALSVGDQTF ADKCLDKMNE FKERGKTIFF ISHSIGQVKS FCEKALWLEY GEVRGYGTVA EIIPQYEKFL KE YRAMSDK EKRQYKERVM RKQQGEFLQA AVK |
-Macromolecule #2: TarG
Macromolecule | Name: TarG / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 33.066285 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGHHHHHHHH HHMRSAVTVL MEHIRNLYLI RRLSLFELKS DNSNQYLGIL WEIINPMIQI AIYWFVFGYG IRGRHPVGHI PFILWMLAG MTVWFFVNQA VLQASKSVYT RIRMVAQMNF PISVIPTYVI TAKFYQHLML LAVIFIIFQF TPYHVSVYLV Q LPYYMFGL ...String: MGHHHHHHHH HHMRSAVTVL MEHIRNLYLI RRLSLFELKS DNSNQYLGIL WEIINPMIQI AIYWFVFGYG IRGRHPVGHI PFILWMLAG MTVWFFVNQA VLQASKSVYT RIRMVAQMNF PISVIPTYVI TAKFYQHLML LAVIFIIFQF TPYHVSVYLV Q LPYYMFGL LALLVSFSLI TSTLATVVRD VQMIVQSLVR ILLYLTPLLW DPSHLPHLVQ VIMRLNPLYY IVEGYRSALL GT SWYLVDH ASYTVYFWVV VILFFVFGSM VHLKFRAHFV DYM |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 8 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: RANDOM CONICAL TILT |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 95416 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL / Overall B value: 198.567 |
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Output model | ![]() PDB-6jbh: |