6GV1 | pdb_00006gv1

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

• PDB DOI: https://doi.org/10.2210/pdb6GV1/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli K-12, Mus musculus
• Expression System: Escherichia coli, Mus musculus
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2018-06-20 Released: 2018-10-03 
• Deposition Author(s): Nagarathinam, K., Parthier, C., Stubbs, M.T., Tanabe, M.
• Funding Organization(s): Other government, Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.283 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.258 (Depositor), 0.262 (DCC) 
• R-Value Observed: 
  0.259 (Depositor) 

Starting Models: experimental

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

• PubMed: 30275448 
• DOI: https://doi.org/10.1038/s41467-018-06306-x
• Primary Citation Related Structures: 
  6GV1


• 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) 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.

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Organizational Affiliation: 
• ZIK HALOmem, Kurt-Mothes-Straße 3, D-06120, Halle/Saale, Germany.
Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther Universität Halle-Wittenberg, Kurt-Mothes-Straße 3a, D-06120, Halle/Saale, Germany.
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.
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.
Advanced Science Research Center, Okayama University, 1-1-1 Kita-ku, Tsushima-naka, Okayama, 700-8530, Japan.
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.
RIKEN, SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.
ZIK HALOmem, Kurt-Mothes-Straße 3, D-06120, Halle/Saale, Germany. [e-mail].
Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther Universität Halle-Wittenberg, Kurt-Mothes-Straße 3a, D-06120, Halle/Saale, Germany. [e-mail].
ZIK HALOmem, Kurt-Mothes-Straße 3, D-06120, Halle/Saale, Germany. [e-mail].
Structural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: surface plasmon resonance, gel filtration

Macromolecule Content 

• Total Structure Weight: 93.06 kDa 
• Atom Count: 6,139 
• Modeled Residue Count: 806 
• Deposited Residue Count: 860 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major Facilitator Superfamily multidrug/H+ antiporter MdfA from E.coli	A	410	Escherichia coli K-12	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0AEY8 (Escherichia coli (strain K12)) Explore P0AEY8  Go to UniProtKB:  P0AEY8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment YN1074 heavy chain	B [auth H]	236	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment YN1074 light chain	C [auth L]	214	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.283 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.258 (Depositor), 0.262 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.258	α = 90
b = 73.258	β = 90
c = 927.92	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-10-03 
Deposition Author(s): Nagarathinam, K., Parthier, C., Stubbs, M.T., Tanabe, M.

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Funding Organization	Location	Grant Number
Other government	Germany	BMBF 03Z2HN21
Japan Agency for Medical Research and Development (AMED)	Japan	JP18am0101071j0001

Revision History  

• Version 1.0: 2018-10-03
  Type: Initial release
  
• Version 1.1: 2018-10-10
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-10-09
  Changes: Structure summary