5EGI

Structure of a Trimeric Intracellular Cation channel from C. elegans with bound Ca2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.263 

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Ligand Structure Quality Assessment 


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Literature

Pore architecture of TRIC channels and insights into their gating mechanism.

Yang, H.T.Hu, M.H.Guo, J.L.Ou, X.M.Cai, T.X.Liu, Z.F.

(2016) Nature 538: 537-541

  • DOI: https://doi.org/10.1038/nature19767
  • Primary Citation of Related Structures:  
    5EGI, 5EIK

  • PubMed Abstract: 

    Intracellular Ca 2+ signalling processes are fundamental to muscle contraction, neurotransmitter release, cell growth and apoptosis. Release of Ca 2+ from the intracellular stores is supported by a series of ion channels in sarcoplasmic or endoplasmic reticulum (SR/ER). Among them, two isoforms of the trimeric intracellular cation (TRIC) channel family, named TRIC-A and TRIC-B, modulate the release of Ca 2+ through the ryanodine receptor or inositol triphosphate receptor, and maintain the homeostasis of ions within SR/ER lumen. Genetic ablations or mutations of TRIC channels are associated with hypertension, heart disease, respiratory defects and brittle bone disease. Despite the pivotal function of TRIC channels in Ca 2+ signalling, their pore architectures and gating mechanisms remain unknown. Here we present the structures of TRIC-B1 and TRIC-B2 channels from Caenorhabditis elegans in complex with endogenous phosphatidylinositol-4,5-biphosphate (PtdIns(4,5)P 2 , also known as PIP 2 ) lipid molecules. The TRIC-B1/B2 proteins and PIP 2 assemble into a symmetrical homotrimeric complex. Each monomer contains an hourglass-shaped hydrophilic pore contained within a seven-transmembrane-helix domain. Structural and functional analyses unravel the central role of PIP 2 in stabilizing the cytoplasmic gate of the ion permeation pathway and reveal a marked Ca 2+ -induced conformational change in a cytoplasmic loop above the gate. A mechanistic model has been proposed to account for the complex gating mechanism of TRIC channels.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein Y57A10A.10
A, B, C
257Caenorhabditis elegansMutation(s): 0 
Gene Names: CELE_Y57A10A.10Y57A10A.10
Membrane Entity: Yes 
UniProt
Find proteins for Q9NA75 (Caenorhabditis elegans)
Explore Q9NA75 
Go to UniProtKB:  Q9NA75
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NA75
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PT5
Query on PT5

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
G [auth C]
[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate
C47 H85 O19 P3
CNWINRVXAYPOMW-HJBQCNPJSA-N
DMU
Query on DMU

Download Ideal Coordinates CCD File 
H [auth C]DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.263 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.05α = 90
b = 102.05β = 90
c = 279.99γ = 90
Software Package:
Software NamePurpose
CNSrefinement
iMOSFLMdata reduction
SCALAdata scaling
AutoSolphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National 973 projectChina2014CB910301
Chinese Academy of SciencesChinaXDB08020302

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2017-10-04
    Changes: Data collection, Derived calculations
  • Version 1.2: 2019-12-25
    Changes: Database references
  • Version 2.0: 2024-03-20
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary