6GV1

Crystal structure of E.coli Multidrug/H+ antiporter MdfA in outward open conformation with bound Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Outward open conformation of a Major Facilitator Superfamily multidrug/H+antiporter provides insights into switching mechanism.

Nagarathinam, K.Nakada-Nakura, Y.Parthier, C.Terada, T.Juge, N.Jaenecke, F.Liu, K.Hotta, Y.Miyaji, T.Omote, H.Iwata, S.Nomura, N.Stubbs, M.T.Tanabe, M.

(2018) Nat Commun 9: 4005-4005

  • DOI: 10.1038/s41467-018-06306-x

  • PubMed Abstract: 
  • Multidrug resistance (MDR) poses a major challenge to medicine. A principle cause of MDR is through active efflux by MDR transporters situated in the bacterial membrane. Here we present the crystal structure of the major facilitator superfamily (MFS) ...

    Multidrug resistance (MDR) poses a major challenge to medicine. A principle cause of MDR is through active efflux by MDR transporters situated in the bacterial membrane. Here we present the crystal structure of the major facilitator superfamily (MFS) drug/H + antiporter MdfA from Escherichia coli in an outward open conformation. Comparison with the inward facing (drug binding) state shows that, in addition to the expected change in relative orientations of the N- and C-terminal lobes of the antiporter, the conformation of TM5 is kinked and twisted. In vitro reconstitution experiments demonstrate the importance of selected residues for transport and molecular dynamics simulations are used to gain insights into antiporter switching. With the availability of structures of alternative conformational states, we anticipate that MdfA will serve as a model system for understanding drug efflux in MFS MDR antiporters.


    Related Citations: 
    • The multidrug-resistance transporter MdfA from Escherichia coli: crystallization and X-ray diffraction analysis.
      Nagarathinam, K.,Jaenecke, F.,Nakada-Nakura, Y.,Hotta, Y.,Liu, K.,Iwata, S.,Stubbs, M.T.,Nomura, N.,Tanabe, M.
      (2017) Acta Crystallogr F Struct Biol Commun 73: 423


    Organizational Affiliation

    ZIK HALOmem, Kurt-Mothes-Straße 3, D-06120, Halle/Saale, Germany. mikio.tanabe@kek.jp.,Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,ZIK HALOmem, Kurt-Mothes-Straße 3, D-06120, Halle/Saale, Germany.,Structural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan. mikio.tanabe@kek.jp.,Institute of Virology, Hannover Medical School, Carl-Neuberg-Straße 1, D-30625, Hannover, Germany.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan.,Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther Universität Halle-Wittenberg, Kurt-Mothes-Straße 3a, D-06120, Halle/Saale, Germany.,Department of Membrane Biochemistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1 Kita-ku, Tsushima-naka, Okayama, 700-8530, Japan.,Advanced Science Research Center, Okayama University, 1-1-1 Kita-ku, Tsushima-naka, Okayama, 700-8530, Japan.,Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther Universität Halle-Wittenberg, Kurt-Mothes-Straße 3a, D-06120, Halle/Saale, Germany. stubbs@biochemtech.uni-halle.de.,ZIK HALOmem, Kurt-Mothes-Straße 3, D-06120, Halle/Saale, Germany. stubbs@biochemtech.uni-halle.de.,RIKEN, SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major Facilitator Superfamily multidrug/H+ antiporter MdfA from E.coli
A
410Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: mdfA (cmlA, cmr)
Find proteins for P0AEY8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEY8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab fragment YN1074 heavy chain
H
236N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab fragment YN1074 light chain
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.258 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 73.258α = 90.00
b = 73.258β = 90.00
c = 927.920γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentGermanyBMBF 03Z2HN21
Japan Agency for Medical Research and Development (AMED)JapanJP18am0101071j0001

Revision History 

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2018-10-10
    Type: Data collection, Database references, Structure summary