Structural and Functional Characterization of a Calcium-activated Cation channel from Tsukamurella Paurometabola

Experimental Data Snapshot

  • Resolution: 3.61 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola.

Dhakshnamoorthy, B.Rohaim, A.Rui, H.Blachowicz, L.Roux, B.

(2016) Nat Commun 7: 12753-12753

  • DOI: https://doi.org/10.1038/ncomms12753
  • Primary Citation of Related Structures:  
    5CBF, 5CBG, 5CBH

  • PubMed Abstract: 

    The selectivity filter is an essential functional element of K + channels that is highly conserved both in terms of its primary sequence and its three-dimensional structure. Here, we investigate the properties of an ion channel from the Gram-positive bacterium Tsukamurella paurometabola with a selectivity filter formed by an uncommon proline-rich sequence. Electrophysiological recordings show that it is a non-selective cation channel and that its activity depends on Ca 2+ concentration. In the crystal structure, the selectivity filter adopts a novel conformation with Ca 2+ ions bound within the filter near the pore helix where they are coordinated by backbone oxygen atoms, a recurrent motif found in multiple proteins. The binding of Ca 2+ ion in the selectivity filter controls the widening of the pore as shown in crystal structures and in molecular dynamics simulations. The structural, functional and computational data provide a characterization of this calcium-gated cationic channel.

  • Organizational Affiliation

    Division of Biological Sciences, Department of Biochemistry and Molecular Biology, The University of Chicago 929 East 57th Street Chicago, Illinois 60637, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ion transport 2 domain protein
A, B, C, D, E
A, B, C, D, E, F
129Tsukamurella paurometabola DSM 20162Mutation(s): 0 
Gene Names: Tpau_1687
Membrane Entity: Yes 
Find proteins for D5UM26 (Tsukamurella paurometabola (strain ATCC 8368 / DSM 20162 / CCUG 35730 / CIP 100753 / JCM 10117 / KCTC 9821 / NBRC 16120 / NCIMB 702349 / NCTC 13040))
Explore D5UM26 
Go to UniProtKB:  D5UM26
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5UM26
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.61 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.053α = 90
b = 116.053β = 90
c = 132.581γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
Cootmodel building
HKL-2000data 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 StatesR01-GM062342

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.3: 2018-03-07
    Changes: Database references, Structure summary
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description