5NSW

Xenon for tunnelling analysis of the efflux pump component OprN.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Xenon for tunnelling analysis of the efflux pump component OprN.

Ntsogo Enguene, Y.V.Phan, G.Garnier, C.Ducruix, A.Prange, T.Broutin, I.

(2017) PLoS One 12: e0184045-e0184045

  • DOI: https://doi.org/10.1371/journal.pone.0184045
  • Primary Citation of Related Structures:  
    5IUY, 5NSW

  • PubMed Abstract: 

    Tripartite efflux pumps are among the main actors responsible for antibiotics resistance in Gram-negative bacteria. In the last two decades, structural studies gave crucial information about the assembly interfaces and the mechanistic motions. Thus rigidifying the assembly seems to be an interesting way to hamper the drug efflux. In this context, xenon is a suitable probe for checking whether small ligands could act as conformational lockers by targeting hydrophobic cavities. Here we focus on OprN, the outer membrane channel of the MexEF efflux pump from Pseudomonas aeruginosa. After exposing OprN crystals to xenon gas pressure, 14 binding sites were observed using X-ray crystallography. These binding sites were unambiguously characterized in hydrophobic cavities of OprN. The major site is observed in the sensitive iris-like region gating the channel at the periplasmic side, built by the three key-residues Leu 405, Asp 109, and Arg 412. This arrangement defines along the tunnel axis a strong hydrophobic/polar gradient able to enhance the passive efflux mechanism of OprN. The other xenon atoms reveal strategic hydrophobic regions of the channel scaffold to target, with the aim to freeze the dynamic movements responsible of the open/close conformational equilibrium in OprN.


  • Organizational Affiliation

    Laboratoire de Cristallographie et RMN Biologiques (UMR 8015, CNRS), Faculté de Pharmacie, Université Paris Descartes, USPC, Paris, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Multidrug efflux outer membrane protein OprN
A, B, C
453Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: oprNPA2495
Membrane Entity: Yes 
UniProt
Find proteins for Q9I0Y7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I0Y7 
Go to UniProtKB:  Q9I0Y7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I0Y7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BOG
Query on BOG

Download Ideal Coordinates CCD File 
FA [auth C],
L [auth A],
V [auth B],
W [auth B]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
PLM
Query on PLM

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
Q [auth B]
R [auth B]
Y [auth C]
D [auth A],
E [auth A],
Q [auth B],
R [auth B],
Y [auth C],
Z [auth C]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
XE
Query on XE

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
F [auth A]
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
N [auth B],
O [auth B],
P [auth B],
S [auth B],
T [auth B],
U [auth B],
X [auth C]
XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
AA [auth C]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
NA
Query on NA

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M [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 256.412α = 90
b = 256.412β = 90
c = 81.395γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-12-BSV8-0010-01

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Data collection, Derived calculations
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary