5H36

Crystal structures of the TRIC trimeric intracellular cation channel orthologue from Rhodobacter sphaeroides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.41 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.263 

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Literature

Crystal structures of the TRIC trimeric intracellular cation channel orthologues

Kasuya, G.Hiraizumi, M.Maturana, A.D.Kumazaki, K.Fujiwara, Y.Liu, K.Nakada-Nakura, Y.Iwata, S.Tsukada, K.Komori, T.Uemura, S.Goto, Y.Nakane, T.Takemoto, M.Kato, H.E.Yamashita, K.Wada, M.Ito, K.Ishitani, R.Hattori, M.Nureki, O.

(2016) Cell Res 26: 1288-1301

  • DOI: https://doi.org/10.1038/cr.2016.140
  • Primary Citation of Related Structures:  
    5H35, 5H36

  • PubMed Abstract: 

    Ca 2+ release from the sarcoplasmic reticulum (SR) and endoplasmic reticulum (ER) is crucial for muscle contraction, cell growth, apoptosis, learning and memory. The trimeric intracellular cation (TRIC) channels were recently identified as cation channels balancing the SR and ER membrane potentials, and are implicated in Ca 2+ signaling and homeostasis. Here we present the crystal structures of prokaryotic TRIC channels in the closed state and structure-based functional analyses of prokaryotic and eukaryotic TRIC channels. Each trimer subunit consists of seven transmembrane (TM) helices with two inverted repeated regions. The electrophysiological, biochemical and biophysical analyses revealed that TRIC channels possess an ion-conducting pore within each subunit, and that the trimer formation contributes to the stability of the protein. The symmetrically related TM2 and TM5 helices are kinked at the conserved glycine clusters, and these kinks are important for the channel activity. Furthermore, the kinks of the TM2 and TM5 helices generate lateral fenestrations at each subunit interface. Unexpectedly, these lateral fenestrations are occupied with lipid molecules. This study provides the structural and functional framework for the molecular mechanism of this ion channel superfamily.


  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein TRICA [auth E],
B [auth A]
215Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Gene Names: RSP_3856
Membrane Entity: Yes 
UniProt
Find proteins for Q3HKN0 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3HKN0 
Go to UniProtKB:  Q3HKN0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3HKN0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PX4
Query on PX4

Download Ideal Coordinates CCD File 
C [auth E],
D [auth A]
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.41 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.263 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.01α = 90
b = 156.01β = 90
c = 82.37γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
SHELXDphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references