6O6J

Crystal structure of the LjCASTOR gating ring in the Ca2+ and Na+ condition

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Lotus japonicus
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-03-06 Released: 2019-09-11 
  • Deposition Author(s): Jiang, Y., Kim, S.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ca2+-regulated Ca2+channels with an RCK gating ring control plant symbiotic associations.

Kim, S.Zeng, W.Bernard, S.Liao, J.Venkateshwaran, M.Ane, J.M.Jiang, Y.

(2019) Nat Commun 10: 3703-3703

  • DOI: https://doi.org/10.1038/s41467-019-11698-5
  • Primary Citation of Related Structures:  
    6O6J, 6O7A, 6O7C

  • PubMed Abstract: 

    A family of plant nuclear ion channels, including DMI1 (Does not Make Infections 1) and its homologs CASTOR and POLLUX, are required for the establishment of legume-microbe symbioses by generating nuclear and perinuclear Ca 2+ spiking. Here we show that CASTOR from Lotus japonicus is a highly selective Ca 2+ channel whose activation requires cytosolic/nucleosolic Ca 2+ , contrary to the previous suggestion of it being a K + channel. Structurally, the cytosolic/nucleosolic ligand-binding soluble region of CASTOR contains two tandem RCK (Regulator of Conductance for K + ) domains, and four subunits assemble into the gating ring architecture, similar to that of large conductance, Ca 2+ -gated K + (BK) channels despite the lack of sequence similarity. Multiple ion binding sites are clustered at two locations within each subunit, and three of them are identified to be Ca 2+ sites. Our in vitro and in vivo assays also demonstrate the importance of these gating-ring Ca 2+ binding sites to the physiological function of CASTOR as well as DMI1.


  • Organizational Affiliation

    Howard Hughes Medical Institute and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ion channel CASTOR554Lotus japonicusMutation(s): 0 
Gene Names: CASTOR
UniProt
Find proteins for Q5H8A6 (Lotus japonicus)
Explore Q5H8A6 
Go to UniProtKB:  Q5H8A6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5H8A6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.234α = 90
b = 125.234β = 90
c = 81.512γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United StatesY.J.
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM079179
Welch FoundationUnited StatesI-1578

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references, Derived calculations