4MLB | pdb_00004mlb

Reverse polarity of binding pocket suggests different function of a MOP superfamily transporter from Pyrococcus furiosus Vc1 (DSM3638)

• PDB DOI: https://doi.org/10.2210/pdb4MLB/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Pyrococcus furiosus
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2013-09-06 Released: 2013-09-25 
• Deposition Author(s): Malviya, V.N., Nonaka, T., Muenke, C., Koepke, J., Michel, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.231 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Inward-facing conformation of a multidrug resistance MATE family transporter.

Zakrzewska, S., Mehdipour, A.R., Malviya, V.N., Nonaka, T., Koepke, J., Muenke, C., Hausner, W., Hummer, G., Safarian, S., Michel, H.

(2019) Proc Natl Acad Sci U S A 116: 12275-12284

• PubMed: 31160466 
• DOI: https://doi.org/10.1073/pnas.1904210116
• Primary Citation Related Structures: 
  4MLB, 6FHZ, 6GWH, 6HFB


• PubMed Abstract: 
  

  Multidrug and toxic compound extrusion (MATE) transporters mediate excretion of xenobiotics and toxic metabolites, thereby conferring multidrug resistance in bacterial pathogens and cancer cells. Structural information on the alternate conformational states and knowledge of the detailed mechanism of MATE transport are of great importance for drug development. However, the structures of MATE transporters are only known in V-shaped outward-facing conformations. Here, we present the crystal structure of a MATE transporter from Pyrococcus furiosus (PfMATE) in the long-sought-after inward-facing state, which was obtained after crystallization in the presence of native lipids. Transition from the outward-facing state to the inward-facing state involves rigid body movements of transmembrane helices (TMs) 2-6 and 8-12 to form an inverted V, facilitated by a loose binding of TM1 and TM7 to their respective bundles and their conformational flexibility. The inward-facing structure of PfMATE in combination with the outward-facing one supports an alternating access mechanism for the MATE family transporters.

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Organizational Affiliation: 
• Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.
Faculty of Microbiology, University of Regensburg, 93053 Regensburg, Germany.
Institute of Biophysics, Goethe University, 60438 Frankfurt am Main, Germany.
Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany; [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 231.85 kDa 
• Atom Count: 14,749 
• Modeled Residue Count: 1,811 
• Deposited Residue Count: 1,968 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PF0708	A, B, C, D	492	Pyrococcus furiosus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q8U2X0 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U2X0  Go to UniProtKB:  Q8U2X0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CXE	AA [auth B], AB [auth D], BA [auth B], BB [auth D], CA [auth B], CB [auth D], DA [auth B], DB [auth D], E [auth A], EA [auth B], EB [auth D], F [auth A], FA [auth B], FB [auth D], G [auth A], GA [auth B], GB [auth D], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], VA [auth C], WA [auth C], X [auth B], XA [auth C], Y [auth B], YA [auth C], Z [auth B], ZA [auth D]	PENTAETHYLENE GLYCOL MONODECYL ETHER C20 H42 O6 QAXPOSPGRHYIHE-UHFFFAOYSA-N
CL	V [auth A], W [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.231 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 219.56	α = 90
b = 94.548	β = 126.47
c = 138.822	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASES	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Malviya, V.N., Nonaka, T., Muenke, C., Koepke, J., Michel, H.

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2014-10-22
  Changes: Structure summary
• Version 1.2: 2018-09-12
  Changes: Data collection, Experimental preparation
• Version 1.3: 2019-06-12
  Changes: Data collection, Database references
• Version 1.4: 2019-08-14
  Changes: Data collection, Database references
• Version 1.5: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description