6CX0

Structure of AtTPC1 D376A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.352 
  • R-Value Work: 0.318 
  • R-Value Observed: 0.320 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural basis for activation of voltage sensor domains in an ion channel TPC1.

Kintzer, A.F.Green, E.M.Dominik, P.K.Bridges, M.Armache, J.P.Deneka, D.Kim, S.S.Hubbell, W.Kossiakoff, A.A.Cheng, Y.Stroud, R.M.

(2018) Proc Natl Acad Sci U S A 115: E9095-E9104

  • DOI: https://doi.org/10.1073/pnas.1805651115
  • Primary Citation of Related Structures:  
    6CX0, 6E1K, 6E1M, 6E1N, 6E1P

  • PubMed Abstract: 

    Voltage-sensing domains (VSDs) couple changes in transmembrane electrical potential to conformational changes that regulate ion conductance through a central channel. Positively charged amino acids inside each sensor cooperatively respond to changes in voltage. Our previous structure of a TPC1 channel captured an example of a resting-state VSD in an intact ion channel. To generate an activated-state VSD in the same channel we removed the luminal inhibitory Ca 2+ -binding site (Ca i 2+ ), which shifts voltage-dependent opening to more negative voltage and activation at 0 mV. Cryo-EM reveals two coexisting structures of the VSD, an intermediate state 1 that partially closes access to the cytoplasmic side but remains occluded on the luminal side and an intermediate activated state 2 in which the cytoplasmic solvent access to the gating charges closes, while luminal access partially opens. Activation can be thought of as moving a hydrophobic insulating region of the VSD from the external side to an alternate grouping on the internal side. This effectively moves the gating charges from the inside potential to that of the outside. Activation also requires binding of Ca 2+ to a cytoplasmic site (Ca a 2+ ). An X-ray structure with Ca a 2+ removed and a near-atomic resolution cryo-EM structure with Ca i 2+ removed define how dramatic conformational changes in the cytoplasmic domains may communicate with the VSD during activation. Together four structures provide a basis for understanding the voltage-dependent transition from resting to activated state, the tuning of VSD by thermodynamic stability, and this channel's requirement of cytoplasmic Ca 2+ ions for activation.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Two pore calcium channel protein 1727Arabidopsis 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.352 
  • R-Value Work: 0.318 
  • R-Value Observed: 0.320 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.47α = 90
b = 154.42β = 90
c = 218.45γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

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 StatesGM24485

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description