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 6JBH | pdb_00006jbh

Cryo-EM structure and transport mechanism of a wall teichoic acid ABC transporter


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6JBH

This is version 1.3 of the entry. See complete history. 

Literature

Cryo-electron Microscopy Structure and Transport Mechanism of a Wall Teichoic Acid ABC Transporter.

Chen, L., Hou, W.T., Fan, T., Liu, B., Pan, T., Li, Y.H., Jiang, Y.L., Wen, W., Chen, Z.P., Sun, L., Zhou, C.Z., Chen, Y.

(2020) mBio 11

  • DOI: https://doi.org/10.1128/mBio.02749-19
  • Primary Citation Related Structures: 
    6JBH

  • PubMed Abstract: 

    The wall teichoic acid (WTA) is a major cell wall component of Gram-positive bacteria, such as methicillin-resistant Staphylococcus aureus (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 Alicyclobacillus herbarius 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. IMPORTANCE The wall teichoic acid (WTA) is a major component of cell wall and a pathogenic factor in methicillin-resistant Staphylococcus aureus (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.


  • Organizational Affiliation: 
    • Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.

Macromolecule Content 

  • Total Structure Weight: 126.54 kDa 
  • Atom Count: 8,592 
  • Modeled Residue Count: 1,062 
  • Deposited Residue Count: 1,100 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TarH
A, B
270Paenalicyclobacillus herbariusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A6I8WFL6 (Paenalicyclobacillus herbarius)
Explore A0A6I8WFL6 
Go to UniProtKB:  A0A6I8WFL6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6I8WFL6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TarG
C, D
280Paenalicyclobacillus herbariusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A6I8WFL7 (Paenalicyclobacillus herbarius)
Explore A0A6I8WFL7 
Go to UniProtKB:  A0A6I8WFL7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6I8WFL7
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina2015CB910103

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references
  • Version 1.3: 2025-06-18
    Changes: Data collection, Structure summary