4MLB

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


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

  • DOI: https://doi.org/10.1073/pnas.1904210116
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PF0708
A, B, C, D
492Pyrococcus furiosusMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U2X0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CXE
Query on CXE

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth D]
BA [auth B]
BB [auth D]
CA [auth B]
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
Query on CL

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 219.56α = 90
b = 94.548β = 126.47
c = 138.822γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASESphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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