Cryo-EM structure of human TPC2 channel in the apo state

Experimental Data Snapshot

  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

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Structural mechanisms of phospholipid activation of the human TPC2 channel.

She, J.Zeng, W.Guo, J.Chen, Q.Bai, X.Jiang, Y.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.45222
  • Primary Citation of Related Structures:  
    6NQ0, 6NQ1, 6NQ2

  • PubMed Abstract: 

    Mammalian two-pore channels (TPCs) regulate the physiological functions of the endolysosome. Here we present cryo-EM structures of human TPC2 (HsTPC2), a phosphatidylinositol 3,5-bisphosphate (PI(3,5)P 2 )-activated, Na + selective channel, in the ligand-bound and apo states. The apo structure captures the closed conformation, while the ligand-bound form features the channel in both open and closed conformations. Combined with functional analysis, these structures provide insights into the mechanism of PI(3,5)P 2 -regulated gating of TPC2, which is distinct from that of TPC1. Specifically, the endolysosome-specific PI(3,5)P 2 binds at the first 6-TM and activates the channel - independently of the membrane potential - by inducing a structural change at the pore-lining inner helix (IS6), which forms a continuous helix in the open state but breaks into two segments at Gly317 in the closed state. Additionally, structural comparison to the voltage-dependent TPC1 structure allowed us to identify Ile551 as being responsible for the loss of voltage dependence in TPC2.

  • Organizational Affiliation

    Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Two pore calcium channel protein 2
A, B
756Homo sapiensMutation(s): 0 
Gene Names: TPCN2TPC2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NHX9 (Homo sapiens)
Explore Q8NHX9 
Go to UniProtKB:  Q8NHX9
GTEx:  ENSG00000162341 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NHX9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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
Howard Hughes Medical Institute (HHMI)United States--
Welch FoundationGrant I-1578
Other governmentthe Cancer Prevention and Research Initiative of Texas

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Author supporting evidence