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- PDB-6nq1: Cryo-EM structure of human TPC2 channel in the apo state -

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Basic information

Entry
Database: PDB / ID: 6nq1
TitleCryo-EM structure of human TPC2 channel in the apo state
ComponentsTwo pore calcium channel protein 2
KeywordsTRANSPORT PROTEIN / channel / lysosome
Function / homology
Function and homology information


endosome to lysosome transport of low-density lipoprotein particle / negative regulation of developmental pigmentation / intracellular pH reduction / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / NAADP-sensitive calcium-release channel activity / regulation of exocytosis / melanosome membrane / endolysosome membrane / phosphatidylinositol-3,5-bisphosphate binding / response to vitamin D ...endosome to lysosome transport of low-density lipoprotein particle / negative regulation of developmental pigmentation / intracellular pH reduction / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / NAADP-sensitive calcium-release channel activity / regulation of exocytosis / melanosome membrane / endolysosome membrane / phosphatidylinositol-3,5-bisphosphate binding / response to vitamin D / ligand-gated sodium channel activity / lysosome organization / smooth muscle contraction / monoatomic ion channel complex / voltage-gated calcium channel activity / receptor-mediated endocytosis of virus by host cell / release of sequestered calcium ion into cytosol / sodium ion transmembrane transport / calcium-mediated signaling / calcium channel activity / Stimuli-sensing channels / intracellular calcium ion homeostasis / late endosome membrane / monoatomic ion transmembrane transport / lysosome / endosome membrane / regulation of autophagy / endocytosis involved in viral entry into host cell / lysosomal membrane / protein kinase binding / identical protein binding / cytosol
Similarity search - Function
Two pore channel protein 2 / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Two pore channel protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsShe, J. / Zeng, W. / Guo, J. / Chen, Q. / Bai, X. / Jiang, Y.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079179 United States
Howard Hughes Medical Institute (HHMI) United States
Welch FoundationGrant I-1578
Other governmentthe Cancer Prevention and Research Initiative of Texas
CitationJournal: Elife / Year: 2019
Title: Structural mechanisms of phospholipid activation of the human TPC2 channel.
Authors: Ji She / Weizhong Zeng / Jiangtao Guo / Qingfeng Chen / Xiao-Chen Bai / Youxing Jiang /
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) ...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)-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-regulated gating of TPC2, which is distinct from that of TPC1. Specifically, the endolysosome-specific PI(3,5)P 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.
History
DepositionJan 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.0Mar 27, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 27, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 27, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 27, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 27, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 27, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 27, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 27, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 27, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update
Revision 1.3May 14, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 14, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Assembly

Deposited unit
A: Two pore calcium channel protein 2
B: Two pore calcium channel protein 2


Theoretical massNumber of molelcules
Total (without water)171,3442
Polymers171,3442
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area8770 Å2
ΔGint-90 kcal/mol
Surface area64570 Å2

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Components

#1: Protein Two pore calcium channel protein 2 / Voltage-dependent calcium channel protein TPC2


Mass: 85671.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPCN2, TPC2 / Production host: Homo sapiens (human) / References: UniProt: Q8NHX9
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Two-pore channel 2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96361 / Symmetry type: POINT

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