4ZP0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/cr.2015.94
  • Primary Citation of Related Structures:  

  • 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 ...

    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.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.,College of Biotechnology, Tianjin University of Science and Technology, 29 13th Street, TEDA, Tianjin 300457, China.,University of Chinese Academy of Sciences, Beijing 100049, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Multidrug transporter MdfA
A
392Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: mdfA (cmlA, cmr)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Major Facilitator Superfamily (MFS) Transporters
Protein: 
MdfA multidrug resistance transporter in complex with deoxycholate
Find proteins for P0AEY8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEY8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LDA
Query on LDA

Download SDF File 
Download CCD File 
A
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
DXC
Query on DXC

Download SDF File 
Download CCD File 
A
(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
DEOXYCHOLIC ACID
C24 H40 O4
KXGVEGMKQFWNSR-LLQZFEROSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 94.652α = 90.00
b = 64.235β = 110.02
c = 101.350γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
SHELXDEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and TechnologyChina2011CB910301

Revision History 

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2015-09-16
    Type: Database references