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- PDB-9kcv: Structure of the Medicago truncatula CNGC15b with CAM -

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Basic information

Entry
Database: PDB / ID: 9kcv
TitleStructure of the Medicago truncatula CNGC15b with CAM
ComponentsProtein CNGC15b,Calmodulin 2
KeywordsMEMBRANE PROTEIN / channel
Function / homology
Function and homology information


arbuscular mycorrhizal association / nodulation / voltage-gated potassium channel activity / enzyme regulator activity / calcium channel activity / nuclear membrane / transmembrane transporter binding / calcium ion binding / cytoplasm
Similarity search - Function
Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / : / RmlC-like jelly roll fold / EF-hand domain pair / EF-hand, calcium binding motif ...Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / : / RmlC-like jelly roll fold / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
Protein CNGC15b / Calmodulin 2
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsYang, G.H. / Xu, X. / Yang, J.Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32422038 China
National Natural Science Foundation of China (NSFC)32171188 China
CitationJournal: Cell Discov / Year: 2025
Title: Structural basis for the activity regulation of Medicago calcium channel CNGC15.
Authors: Xia Xu / Qinrui Wang / Tengfei Sun / Heyi Gao / Ruichu Gu / Junzhao Yang / Jiaqi Zhou / Peng Fu / Han Wen / Guanghui Yang /
Abstract: Cyclic nucleotide-gated ion channels (CNGCs) in plants mediate Ca influx in response to environmental changes. Among numerous plant CNGCs, Medicago truncatula CNGC15a/b/c (MtCNGC15) is localized to ...Cyclic nucleotide-gated ion channels (CNGCs) in plants mediate Ca influx in response to environmental changes. Among numerous plant CNGCs, Medicago truncatula CNGC15a/b/c (MtCNGC15) is localized to the nuclear envelope. The opening and closing cycle of MtCNGC15 is tightly associated with the Ca oscillation in symbiosis. However, the molecular mechanism underlying MtCNGC15 activity regulation remains unclear. In this study, we present the structures of MtCNGC15 in its apo form and in the presence of CaM. The apo MtCNGC15b exhibits a flexible cytoplasmic domain (CPD), whereas binding of the MtCaM inhibits Ca currents and stabilizes the highly dynamic CPD. Furthermore, the activity of MtCNGC15b seems to be independent of cGMP. The hypothetical binding pocket for cGMP is occupied by an arginine residue. These findings elucidate the structural basis for the activity regulation of nuclear localized MtCNGC15.
History
DepositionNov 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein CNGC15b,Calmodulin 2
B: Protein CNGC15b,Calmodulin 2
C: Protein CNGC15b,Calmodulin 2
D: Protein CNGC15b,Calmodulin 2


Theoretical massNumber of molelcules
Total (without water)363,2574
Polymers363,2574
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Protein CNGC15b,Calmodulin 2 / Cyclic nucleotide-gated ion channel protein 15 b / EF hand calcium-binding family protein / ...Cyclic nucleotide-gated ion channel protein 15 b / EF hand calcium-binding family protein / Putative EF-hand domain pair protein


Mass: 90814.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic)
Gene: CNGC15B, MTR_4g058730, 11431828, MTR_5g088320, MtrunA17_Chr5g0440931
Production host: Homo sapiens (human) / References: UniProt: G7JND3, UniProt: Q71JC5
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: homotetrameric channel / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Medicago truncatula (barrel medic)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
8PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117605 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00217156
ELECTRON MICROSCOPYf_angle_d0.5523308
ELECTRON MICROSCOPYf_dihedral_angle_d3.7372272
ELECTRON MICROSCOPYf_chiral_restr0.0392672
ELECTRON MICROSCOPYf_plane_restr0.0032912

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