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- EMDB-9790: Cryo-EM structure and transport mechanism of a wall teichoic acid... -

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Basic information

Entry
Database: EMDB / ID: EMD-9790
TitleCryo-EM structure and transport mechanism of a wall teichoic acid ABC transporter
Map data
Sample
  • Complex: wall teichoic acid ABC transporter TarGH
    • Protein or peptide: TarH
    • Protein or peptide: TarG
KeywordsABC Transporter / TRANSPORT PROTEIN
Biological speciesAlicyclobacillus herbarius (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsChen L / Hou WT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China2015CB910103 China
CitationJournal: 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
DepositionJan 25, 2019-
Header (metadata) releaseMar 4, 2020-
Map releaseMar 4, 2020-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jbh
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9790.png

Downloads & links

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Map

FileDownload / File: emd_9790.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 200 pix.
= 272. Å		1.36 Å/pix.
x 200 pix.
= 272. Å		1.36 Å/pix.
x 200 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.16621928 - 0.3623965
Average (Standard dev.)0.0006289688 (±0.012150581)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z272.000272.000272.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ336336336
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1660.3620.001

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Supplemental data

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Sample components

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Entire : wall teichoic acid ABC transporter TarGH

EntireName: wall teichoic acid ABC transporter TarGH
Components
  • Complex: wall teichoic acid ABC transporter TarGH
    • Protein or peptide: TarH
    • Protein or peptide: TarG

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Supramolecule #1: wall teichoic acid ABC transporter TarGH

SupramoleculeName: wall teichoic acid ABC transporter TarGH / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Alicyclobacillus herbarius (bacteria)

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Macromolecule #1: TarH

MacromoleculeName: TarH / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Alicyclobacillus herbarius (bacteria)
Molecular weightTheoretical: 30.201881 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: TarG

MacromoleculeName: TarG / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Alicyclobacillus herbarius (bacteria)
Molecular weightTheoretical: 33.066285 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration8 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: RANDOM CONICAL TILT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 95416
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL / Overall B value: 198.567
Output model

PDB-6jbh:
Cryo-EM structure and transport mechanism of a wall teichoic acid ABC transporter

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