6WK5

Crystal structure of Gdx-Clo from Small Multidrug Resistance family of transporters


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report


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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A [auth B],
B [auth A]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.8α = 90
b = 51.093β = 93.08
c = 108.433γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
SHARPphasing
Aimlessdata scaling
DIALSdata reduction

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
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Structure summary