Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 171.34 kDa 
• Atom Count: 10,046 
• Modelled Residue Count: 1,242 
• Deposited Residue Count: 1,512 
• Unique protein chains: 1

 6NQ1

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

• PDB DOI: 10.2210/pdb6NQ1/pdb
• EM Map EMD-0478: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2019-01-18 Released: 2019-03-27 
• Deposition Author(s): She, J., Zeng, W., Guo, J., Chen, Q., Bai, X., Jiang, Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI), Welch Foundation, Other government

---

Experimental Data Snapshot

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

Literature

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

• PubMed: 30860481 
• DOI: 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: 

Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Two pore calcium channel protein 2	A, B	756	Homo sapiens	Mutation(s): 0  Gene Names: TPCN2, TPC2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NHX9 (Homo sapiens) Explore Q8NHX9  Go to UniProtKB:  Q8NHX9
PHAROS:  Q8NHX9

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): She, J., Zeng, W., Guo, J., Chen, Q., Bai, X., Jiang, Y.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM079179
Howard Hughes Medical Institute (HHMI)	United States	--
Welch Foundation		Grant I-1578
Other government		the Cancer Prevention and Research Initiative of Texas

Revision History  

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