5TUA | pdb_00005tua

structure of a Na+-selective mutant of two-pore channel from Arabidopsis thaliana AtTPC1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.323 (Depositor), 0.335 (DCC) 
  • R-Value Work: 
    0.310 (Depositor), 0.313 (DCC) 
  • R-Value Observed: 
    0.311 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5TUA

This is version 1.5 of the entry. See complete history

Literature

Tuning the ion selectivity of two-pore channels.

Guo, J.Zeng, W.Jiang, Y.

(2017) Proc Natl Acad Sci U S A 114: 1009-1014

  • DOI: https://doi.org/10.1073/pnas.1616191114
  • Primary Citation Related Structures: 
    5TUA

  • PubMed Abstract: 

    Organellar two-pore channels (TPCs) contain two copies of a Shaker-like six-transmembrane (6-TM) domain in each subunit and are ubiquitously expressed in plants and animals. Interestingly, plant and animal TPCs share high sequence similarity in the filter region, yet exhibit drastically different ion selectivity. Plant TPC1 functions as a nonselective cation channel on the vacuole membrane, whereas mammalian TPC channels have been shown to be endo/lysosomal Na + -selective or Ca 2+ -release channels. In this study, we performed systematic characterization of the ion selectivity of TPC1 from Arabidopsis thaliana (AtTPC1) and compared its selectivity with the selectivity of human TPC2 (HsTPC2). We demonstrate that AtTPC1 is selective for Ca 2+ over Na + , but nonselective among monovalent cations (Li + , Na + , and K + ). Our results also confirm that HsTPC2 is a Na + -selective channel activated by phosphatidylinositol 3,5-bisphosphate. Guided by our recent structure of AtTPC1, we converted AtTPC1 to a Na + -selective channel by mimicking the selectivity filter of HsTPC2 and identified key residues in the TPC filters that differentiate the selectivity between AtTPC1 and HsTPC2. Furthermore, the structure of the Na + -selective AtTPC1 mutant elucidates the structural basis for Na + selectivity in mammalian TPCs.


  • Organizational Affiliation
    • Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040.

Macromolecule Content 

  • Total Structure Weight: 86.82 kDa 
  • Atom Count: 5,126 
  • Modeled Residue Count: 627 
  • Deposited Residue Count: 739 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Two pore calcium channel protein 1739Arabidopsis thalianaMutation(s): 0 
Gene Names: TPC1CCH1FOU2At4g03560F9H3.19T5L23.5
Membrane Entity: Yes 
UniProt
Find proteins for Q94KI8 (Arabidopsis thaliana)
Explore Q94KI8 
Go to UniProtKB:  Q94KI8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94KI8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BA

Query on BA



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
M [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.323 (Depositor), 0.335 (DCC) 
  • R-Value Work:  0.310 (Depositor), 0.313 (DCC) 
  • R-Value Observed: 0.311 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.535α = 90
b = 156.371β = 90
c = 217.128γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing

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 StatesGM079179
Welch FoundationUnited StatesI-1578
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-02-01
    Changes: Database references
  • Version 1.2: 2017-02-08
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description