6V1Q | pdb_00006v1q

Two-pore channel 3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6V1Q

This is version 1.4 of the entry. See complete history

Literature

Resting state structure of the hyperdepolarization activated two-pore channel 3.

Dickinson, M.S.Myasnikov, A.Eriksen, J.Poweleit, N.Stroud, R.M.

(2020) Proc Natl Acad Sci U S A 117: 1988-1993

  • DOI: https://doi.org/10.1073/pnas.1915144117
  • Primary Citation Related Structures: 
    6V1Q

  • PubMed Abstract: 

    Voltage-gated ion channels endow membranes with excitability and the means to propagate action potentials that form the basis of all neuronal signaling. We determined the structure of a voltage-gated sodium channel, two-pore channel 3 (TPC3), which generates ultralong action potentials. TPC3 is distinguished by activation only at extreme membrane depolarization (V 50 ∼ +75 mV), in contrast to other TPCs and Na V channels that activate between -20 and 0 mV. We present electrophysiological evidence that TPC3 voltage activation depends only on voltage sensing domain 2 (VSD2) and that each of the three gating arginines in VSD2 reduces the activation threshold. The structure presents a chemical basis for sodium selectivity, and a constricted gate suggests a closed pore consistent with extreme voltage dependence. The structure, confirmed by our electrophysiology, illustrates the configuration of a bona fide resting state voltage sensor, observed without the need for any inhibitory ligand, and independent of any chemical or mutagenic alteration.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158.

Macromolecule Content 

  • Total Structure Weight: 177.57 kDa 
  • Atom Count: 8,825 
  • Modeled Residue Count: 1,076 
  • Deposited Residue Count: 1,546 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Two pore channel 3
A, B
773Danio rerioMutation(s): 0 
Gene Names: tpcn3gb:eh507706TPC3
Membrane Entity: Yes 
UniProt
Find proteins for C4IXV6 (Danio rerio)
Explore C4IXV6 
Go to UniProtKB:  C4IXV6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4IXV6
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2

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 StatesR01 GM24485

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2020-01-22
    Changes: Database references
  • Version 1.3: 2020-02-12
    Changes: Database references
  • Version 1.4: 2024-03-06
    Changes: Data collection, Database references