4ZOW

Crystal structure of E. coli multidrug transporter MdfA in complex with chloramphenicol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.235 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

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Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history


Literature

Substrate-bound structure of the E. coli multidrug resistance transporter MdfA

Heng, J.Zhao, Y.Liu, M.Liu, Y.Fan, J.Wang, X.Zhao, Y.Zhang, X.C.

(2015) Cell Res 25: 1060-1073

  • DOI: https://doi.org/10.1038/cr.2015.94
  • Primary Citation of Related Structures:  
    4ZOW, 4ZP0, 4ZP2

  • PubMed Abstract: 

    Multidrug resistance is a serious threat to public health. Proton motive force-driven antiporters from the major facilitator superfamily (MFS) constitute a major group of multidrug-resistance transporters. Currently, no reports on crystal structures of MFS antiporters in complex with their substrates exist. The E. coli MdfA transporter is a well-studied model system for biochemical analyses of multidrug-resistance MFS antiporters. Here, we report three crystal structures of MdfA-ligand complexes at resolutions up to 2.0 Å, all in the inward-facing conformation. The substrate-binding site sits proximal to the conserved acidic residue, D34. Our mutagenesis studies support the structural observations of the substrate-binding mode and the notion that D34 responds to substrate binding by adjusting its protonation status. Taken together, our data unveil the substrate-binding mode of MFS antiporters and suggest a mechanism of transport via this group of transporters.


  • Organizational Affiliation

    National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Multidrug transporter MdfA391Escherichia coli K-12Mutation(s): 1 
Gene Names: mdfAcmlAcmrb0842JW0826
Membrane Entity: Yes 
UniProt
Find proteins for P0AEY8 (Escherichia coli (strain K12))
Explore P0AEY8 
Go to UniProtKB:  P0AEY8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEY8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLM
Query on CLM

Download Ideal Coordinates CCD File 
B [auth A]CHLORAMPHENICOL
C11 H12 Cl2 N2 O5
WIIZWVCIJKGZOK-RKDXNWHRSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.235 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.852α = 90
b = 63.449β = 106.09
c = 99.726γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SOLVEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CLMClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2015-09-02
    Changes: Data collection
  • Version 1.2: 2015-09-16
    Changes: Database references
  • Version 1.3: 2020-02-19
    Changes: Data collection, Derived calculations
  • Version 1.4: 2024-03-20
    Changes: Data collection, Database references