6O6J | pdb_00006o6j

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

• PDB DOI: https://doi.org/10.2210/pdb6O6J/pdb

• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.188 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

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

• PubMed: 31420535 
• DOI: https://doi.org/10.1038/s41467-019-11698-5
• Primary Citation 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.

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Organizational Affiliation: 
• Howard Hughes Medical Institute and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
School of Agriculture, University of Wisconsin-Platteville, Platteville, WI, USA.
Howard Hughes Medical Institute and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA. [e-mail].
Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 62.15 kDa 
• Atom Count: 4,524 
• Modeled Residue Count: 505 
• Deposited Residue Count: 554 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ion channel CASTOR	A	554	Lotus japonicus	Mutation(s): 0  Gene Names: CASTOR
UniProt
Find proteins for Q5H8A6 (Lotus japonicus) Explore Q5H8A6  Go to UniProtKB:  Q5H8A6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)	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 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.234	α = 90
b = 125.234	β = 90
c = 81.512	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Jiang, Y., Kim, S.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	Y.J.
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM079179
Welch Foundation	United States	I-1578

Revision History  

• 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