5CBG | pdb_00005cbg

Calcium activated non-selective cation channel


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 
    0.299 (Depositor), 0.310 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DMUClick on this verticalbar to view details

This is version 1.6 of the entry. See complete history


Literature

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.


Macromolecules
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
129Tsukamurella paurometabola DSM 20162Mutation(s): 0 
Gene Names: Tpau_1687
Membrane Entity: Yes 
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DMU
Query on DMU

Download Ideal Coordinates CCD File 
J [auth D],
L [auth E],
M [auth E]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A]
H [auth B]
I [auth C]
K [auth E]
N [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free:  0.299 (Depositor), 0.310 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.573α = 90
b = 115.573β = 90
c = 127.487γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DMUClick on this verticalbar to view details

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: 2018-01-31
    Changes: Experimental preparation
  • Version 1.4: 2018-03-07
    Changes: Database references, Structure summary
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.6: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description