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- EMDB-62262: Structure of the Medicago truncatula CNGC15b with CAM -

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Basic information

Entry
Database: EMDB / ID: EMD-62262
TitleStructure of the Medicago truncatula CNGC15b with CAM
Map data0.12 in chimera
Sample
  • Complex: homotetrameric channel
    • Protein or peptide: Protein CNGC15b,Calmodulin 2
Keywordschannel / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsYang GH / Xu X / Yang JZ
Funding support China, 2 items
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, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62262.png

Downloads & links

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Map

FileDownload / File: emd_62262.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation0.12 in chimera
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 280 pix.
= 291.2 Å		1.04 Å/pix.
x 280 pix.
= 291.2 Å		1.04 Å/pix.
x 280 pix.
= 291.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-1.2926644 - 1.8481214
Average (Standard dev.)0.00096535054 (±0.038315367)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 291.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 0.12 in chimera

Fileemd_62262_additional_1.map
Annotation0.12 in chimera
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 0.12 in chimera

Fileemd_62262_half_map_1.map
Annotation0.12 in chimera
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 0.12 in chimera

Fileemd_62262_half_map_2.map
Annotation0.12 in chimera
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : homotetrameric channel

EntireName: homotetrameric channel
Components
  • Complex: homotetrameric channel
    • Protein or peptide: Protein CNGC15b,Calmodulin 2

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Supramolecule #1: homotetrameric channel

SupramoleculeName: homotetrameric channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Medicago truncatula (barrel medic)

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Macromolecule #1: Protein CNGC15b,Calmodulin 2

MacromoleculeName: Protein CNGC15b,Calmodulin 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Medicago truncatula (barrel medic)
Molecular weightTheoretical: 90.814188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG SMVTPKFMSD LFEGDHLELA KLTSPNGDNG IKFNEKHVAP RVLSRVFSED YKRVKRRRRI FDPRGQTIHQ WNKIFLVAC LISLFVDPLF FYLPIVQDEV CIDIGIAVEV FLIIIRSIAD VFYVIHIFMR FHTAYVAPSS RVFGRGELVI D SSKIASRY ...String:
MDYKDDDDKG SMVTPKFMSD LFEGDHLELA KLTSPNGDNG IKFNEKHVAP RVLSRVFSED YKRVKRRRRI FDPRGQTIHQ WNKIFLVAC LISLFVDPLF FYLPIVQDEV CIDIGIAVEV FLIIIRSIAD VFYVIHIFMR FHTAYVAPSS RVFGRGELVI D SSKIASRY LHKGFFLDFI AALPLPQVLI WIVIPNLGGS TIANTKNVLR FIIIIQYLPR LFLIFPLSSQ IVKATGVVTE TA WAGAAYN LILYMLASHV LGACWYLLSI ERQEACWKSV CKLEESSCQF DFFDCNMVKD SLRVSWFVTS NVTNLCSPNS LFY QFGIYG DAVTSKVTTS AFFNKYFFCL WWGLRNLSSL GQGLLTSTFV GEIMFAIVIA TLGLVLFALL IGNMQTYLQS TTVR LEEWR VKRTDTEQWM HHRQLPQELR QSVRKYDQYK WIATRGVDEE SLLRGLPLDL RRDIKRHLCL ELVRRVPLFD AMDER MLDA ICERLKPALC TENTYLVREG DPVNEMLFII RGNLDSYTTD GGRTGFFNSC RIGPGDFCGE ELLTWALDPR PTMVIP SST RTVKAISEVE AFALIAEDLK FVASQFRRLH SKQLRNKLRF HSHQWRTWAA CFIQVAWRRT IQEKKGSCGG SGGSGGS GG SGGSGGSMAD QLTDEQISEF KEAFSLFDKD GDGCITTKEL GTVMRSLGQN PTEAELQDMI NEVDADGNGT IDFPEFLN L MARKMKDTDS EEELKEAFRV FDKDQNGEIS AAELRHVMTN LGEKLTDEEV DEMIREADVD GDGQINYEEF VKVMMAK

UniProtKB: Protein CNGC15b, Calmodulin 2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 117605
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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