6WK9

Crystal structure of Gdx-Clo from Small Multidrug Resistance family of transporters in complex with octylguanidinium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The structural basis of promiscuity in small multidrug resistance transporters.

Kermani, A.A.Macdonald, C.B.Burata, O.E.Ben Koff, B.Koide, A.Denbaum, E.Koide, S.Stockbridge, R.B.

(2020) Nat Commun 11: 6064-6064

  • DOI: 10.1038/s41467-020-19820-8
  • Primary Citation of Related Structures:  
    6WK5, 6WK9, 6WK8

  • PubMed Abstract: 
  • By providing broad resistance to environmental biocides, transporters from the small multidrug resistance (SMR) family drive the spread of multidrug resistance cassettes among bacterial populations. A fundamental understanding of substrate selectivity by SMR transporters is needed to identify the types of selective pressures that contribute to this process ...

    By providing broad resistance to environmental biocides, transporters from the small multidrug resistance (SMR) family drive the spread of multidrug resistance cassettes among bacterial populations. A fundamental understanding of substrate selectivity by SMR transporters is needed to identify the types of selective pressures that contribute to this process. Using solid-supported membrane electrophysiology, we find that promiscuous transport of hydrophobic substituted cations is a general feature of SMR transporters. To understand the molecular basis for promiscuity, we solved X-ray crystal structures of a SMR transporter Gdx-Clo in complex with substrates to a maximum resolution of 2.3 Å. These structures confirm the family's extremely rare dual topology architecture and reveal a cleft between two helices that provides accommodation in the membrane for the hydrophobic substituents of transported drug-like cations.


    Organizational Affiliation

    Program in Biophysics, University of Michigan, Ann Arbor, MI, 48109, USA. stockbr@umich.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Multidrug resistance protein, SMR familyB [auth A], A [auth B], F [auth E], E [auth F]105Clostridiales bacterium oral taxon 876 str. F0540Mutation(s): 0 
Gene Names: HMPREF1982_00479
Find proteins for U2EQ00 (Clostridiales bacterium oral taxon 876 str. F0540)
Explore U2EQ00 
Go to UniProtKB:  U2EQ00
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
L10 monobodyC, D, G, H91Homo sapiensMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMU
Query on DMU

Download Ideal Coordinates CCD File 
I [auth B], O [auth C], Q [auth F], U [auth G]DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
 Ligand Interaction
U4G
Query on U4G

Download Ideal Coordinates CCD File 
J [auth B] , K [auth B] , L [auth A] , M [auth C] , N [auth C] , P [auth C] , R [auth F] , S [auth F] , 
J [auth B],  K [auth B],  L [auth A],  M [auth C],  N [auth C],  P [auth C],  R [auth F],  S [auth F],  T [auth E],  V [auth G],  W [auth G]
N-octylguanidine
C9 H21 N3
XPYXSZDENRDLKD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.042α = 92.54
b = 75.828β = 90.04
c = 109.123γ = 109.63
Software Package:
Software NamePurpose
PHENIXrefinement
SHELXphasing
SHARPphasing
STARANISOdata reduction
DIALSdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35-GM128768

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 1.1: 2020-12-09
    Changes: Database references