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: 3.40 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 

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
  • Primary Citation of 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 ...

    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: 

    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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major Facilitator Superfamily multidrug/H+ antiporter MdfA from E.coliA410Escherichia coli K-12Mutation(s): 0 
Gene Names: mdfA, cmlA, cmr, b0842, JW0826
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab fragment YN1074 heavy chainB [auth H]236Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab fragment YN1074 light chainC [auth L]214Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.258α = 90
b = 73.258β = 90
c = 927.92γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

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