4LZ9 | pdb_00004lz9

Structure of MATE multidrug transporter DinF-BH in complex with R6G

• PDB DOI: https://doi.org/10.2210/pdb4LZ9/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Halalkalibacterium halodurans C-125
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2013-07-31 Released: 2013-10-23 
• Deposition Author(s): Lu, M., Radchenko, M., Symersky, J., Nie, R., Guo, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 
  0.300 (Depositor), 0.402 (DCC) 
• R-Value Work: 
  0.290 (Depositor), 0.393 (DCC) 
• R-Value Observed: 
  0.300 (Depositor) 

Literature

Structural insights into H(+)-coupled multidrug extrusion by a MATE transporter

Lu, M., Radchenko, M., Symersky, J., Nie, R., Guo, Y.

(2013) Nat Struct Mol Biol 20: 1310-1317

• PubMed: 24141706 
• DOI: https://doi.org/10.1038/nsmb.2687
• Primary Citation Related Structures: 
  4LZ6, 4LZ9


• PubMed Abstract: 
  

  Multidrug and toxic compound extrusion (MATE) transporters contribute to multidrug resistance by coupling the efflux of drugs to the influx of Na(+) or H(+). Known structures of Na(+)-coupled, extracellular-facing MATE transporters from the NorM subfamily revealed 12 membrane-spanning segments related by a quasi-two-fold rotational symmetry and a multidrug-binding cavity situated near the membrane surface. Here we report the crystal structure of an H(+)-coupled MATE transporter from Bacillus halodurans and the DinF subfamily at 3.2-Å resolution, unveiling a surprisingly asymmetric arrangement of 12 transmembrane helices. We also identified a membrane-embedded substrate-binding chamber by combining crystallographic and biochemical analyses. Our studies further suggested a direct competition between H(+) and substrate during DinF-mediated transport and implied how a MATE transporter alternates between its extracellular- and intracellular-facing conformations to propel multidrug extrusion. Collectively, our results demonstrated heretofore-unrecognized mechanistic diversity among MATE transporters.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 49.06 kDa 
• Atom Count: 479 
• Modeled Residue Count: 446 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BH2163 protein	A	446	Halalkalibacterium halodurans C-125	Mutation(s): 0  Gene Names: BH2163 Membrane Entity: Yes
UniProt
Find proteins for Q9KAX3 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KAX3  Go to UniProtKB:  Q9KAX3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RHQ	B [auth A]	RHODAMINE 6G C28 H31 N2 O3 IWWWBRIIGAXLCJ-KRUMMXJUSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free:  0.300 (Depositor), 0.402 (DCC) 
• R-Value Work:  0.290 (Depositor), 0.393 (DCC) 
• R-Value Observed: 0.300 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.181	α = 90
b = 93.887	β = 90
c = 102.267	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-23 
Deposition Author(s): Lu, M., Radchenko, M., Symersky, J., Nie, R., Guo, Y.

Revision History  

• Version 1.0: 2013-10-23
  Type: Initial release
  
• Version 1.1: 2013-11-20
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations