8VGD | pdb_00008vgd

Complex of ExbD with D-box peptide: Tetragonal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 
    0.204 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.187 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8VGD

This is version 1.1 of the entry. See complete history

Literature

Discovery and structural characterization of the D-box, a conserved TonB motif that couples an inner-membrane motor to outer-membrane transport.

Loll, P.J.Grasty, K.C.Shultis, D.D.Guzman, N.J.Wiener, M.C.

(2024) J Biological Chem 300: 105723-105723

  • DOI: https://doi.org/10.1016/j.jbc.2024.105723
  • Primary Citation Related Structures: 
    8VGC, 8VGD

  • PubMed Abstract: 

    Gram-negative bacteria use TonB-dependent transport to take up nutrients from the external environment, employing the Ton complex to import a variety of nutrients that are either scarce or too large to cross the outer membrane unaided. The Ton complex contains an inner-membrane motor (ExbBD) that generates force, as well as nutrient-specific transport proteins on the outer membrane. These two components are coupled by TonB, which transmits the force from the inner to the outer membrane. TonB contains an N-terminus anchored in the inner membrane, a C-terminal domain that binds the outer-membrane transporter, and a proline-rich linker connecting the two. While much is known about the interaction between TonB and outer-membrane transporters, the critical interface between TonB and ExbBD is less well understood. Here, we identify a conserved motif within TonB that we term the D-box, which serves as an attachment point for ExbD. We characterize the interaction between ExbD and the D-box both functionally and structurally, showing that a homodimer of ExbD captures one copy of the D-box peptide via beta-strand recruitment. We additionally show that both the D-box motif and ExbD are conserved in a range of Gram-negative bacteria, including members of the ESKAPE group of pathogens. The ExbD:D-box interaction is likely to represent an important aspect of force transduction between the inner and outer membranes. Given that TonB-dependent transport is an important contributor to virulence, this interaction is an intriguing potential target for novel antibacterial therapies.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA. Electronic address: pjl28@drexel.edu.

Macromolecule Content 

  • Total Structure Weight: 19.45 kDa 
  • Atom Count: 1,274 
  • Modeled Residue Count: 155 
  • Deposited Residue Count: 175 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Biopolymer transport protein ExbD
A, B
83Escherichia coliMutation(s): 0 
Gene Names: exbDEIMP300_23080
UniProt
Find proteins for P0ABV2 (Escherichia coli (strain K12))
Explore P0ABV2 
Go to UniProtKB:  P0ABV2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABV2
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
GLN-PRO-ILE-SER-VAL-THR-MET-VAL-THRC [auth P]9Escherichia coliMutation(s): 0 
UniProt
Find proteins for P02929 (Escherichia coli (strain K12))
Explore P02929 
Go to UniProtKB:  P02929
Entity Groups
UniProt GroupP02929
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free:  0.204 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.187 (DCC) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.01α = 90
b = 49.01β = 90
c = 62.64γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2024-02-14 
  • Deposition Author(s): Loll, P.J.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Database references