6WK8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.260 

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1038/s41467-020-19820-8
  • Primary Citation of Related Structures:  
    6WK5, 6WK8, 6WK9

  • 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. 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

    Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Multidrug resistance protein, SMR familyA [auth B],
B [auth A]
105Clostridiales bacterium oral taxon 876 str. F0540Mutation(s): 0 
Gene Names: HMPREF1982_00479
Membrane Entity: Yes 
UniProt
Find proteins for U2EQ00 (Clostridiales bacterium oral taxon 876 str. F0540)
Explore U2EQ00 
Go to UniProtKB:  U2EQ00
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU2EQ00
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
L10 monobody
C, D
91Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DMU
Query on DMU

Download Ideal Coordinates CCD File 
G [auth A]DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
9PD
Query on 9PD

Download Ideal Coordinates CCD File 
F [auth B]Dodecyldimethylphosphine oxide
C14 H31 O P
SIDULKZCBGMXJL-UHFFFAOYSA-N
PL0 (Subject of Investigation/LOI)
Query on PL0

Download Ideal Coordinates CCD File 
E [auth B]1-phenylguanidine
C7 H9 N3
QRJZGVVKGFIGLI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.260 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.819α = 90
b = 50.507β = 92.18
c = 108.575γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
SHARPphasing
STARANISOdata scaling
DIALSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references