7VM8

Crystal structure of the MtDMI1 gating ring


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.263 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Constitutive activation of a nuclear-localized calcium channel complex in Medicago truncatula.

Liu, H.Lin, J.S.Luo, Z.Sun, J.Huang, X.Yang, Y.Xu, J.Wang, Y.F.Zhang, P.Oldroyd, G.E.D.Xie, F.

(2022) Proc Natl Acad Sci U S A 119: e2205920119-e2205920119

  • DOI: https://doi.org/10.1073/pnas.2205920119
  • Primary Citation of Related Structures:  
    7VM8

  • PubMed Abstract: 

    Nuclear Ca 2+ oscillations allow symbiosis signaling, facilitating plant recognition of beneficial microsymbionts, nitrogen-fixing rhizobia, and nutrient-capturing arbuscular mycorrhizal fungi. Two classes of channels, DMI1 and CNGC15, in a complex on the nuclear membrane, coordinate symbiotic Ca 2+ oscillations. However, the mechanism of Ca 2+ signature generation is unknown. Here, we demonstrate spontaneous activation of this channel complex, through gain-of-function mutations in DMI1 , leading to spontaneous nuclear Ca 2+ oscillations and spontaneous nodulation, in a CNGC15 -dependent manner. The mutations destabilize a hydrogen-bond or salt-bridge network between two RCK domains, with the resultant structural changes, alongside DMI1 cation permeability, activating the channel complex. This channel complex was reconstituted in human HEK293T cell lines, with the resultant calcium influx enhanced by autoactivated DMI1 and CNGC15s. Our results demonstrate the mode of activation of this nuclear channel complex, show that DMI1 and CNGC15 are sufficient to create oscillatory Ca 2+ signals, and provide insights into its native mode of induction.


  • Organizational Affiliation

    National Key Laboratory of Plant Molecular Genetics,Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ion channel DMI1538Medicago truncatulaMutation(s): 0 
Gene Names: DMI1
UniProt
Find proteins for Q6RHR6 (Medicago truncatula)
Explore Q6RHR6 
Go to UniProtKB:  Q6RHR6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6RHR6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.263 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.982α = 90
b = 110.982β = 90
c = 91.6γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-24
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description