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- EMDB-61105: Cryo-EM structure of Arabidopsis CNGC1 -

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Basic information

Entry
Database: EMDB / ID: EMD-61105
TitleCryo-EM structure of Arabidopsis CNGC1
Map data
Sample
  • Complex: Structure of CNGC1 in GDN
    • Protein or peptide: Cyclic nucleotide-gated ion channel 1
  • Ligand: CALCIUM ION
  • Ligand: water
KeywordsCryo-EM / Membrane protein / polymer / PLANT PROTEIN
Function / homology
Function and homology information


monoatomic ion channel activity / cGMP binding / cAMP binding / calmodulin binding / plasma membrane
Similarity search - Function
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 / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Cyclic nucleotide-gated ion channel 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.51 Å
AuthorsWang JP / Zhang P / Zhang X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32025020 China
CitationJournal: Nat Plants / Year: 2025
Title: Cryo-EM structures of Arabidopsis CNGC1 and CNGC5 reveal molecular mechanisms underlying gating and calcium selectivity.
Authors: Jianping Wang / Bo-Ya Du / Xue Zhang / Xiaomin Qu / Yang Yang / Zhao Yang / Yong-Fei Wang / Peng Zhang /
Abstract: Plant cyclic nucleotide-gated channels (CNGCs) belong to the cyclic nucleotide-binding domain (CNBD) channel family, but are phylogenetically classified in a distinct branch. In contrast to their ...Plant cyclic nucleotide-gated channels (CNGCs) belong to the cyclic nucleotide-binding domain (CNBD) channel family, but are phylogenetically classified in a distinct branch. In contrast to their animal counterparts of K-selective or non-selective cation channels, plant CNGCs mainly mediate Ca influx and are involved in various physiological processes, such as stomatal movements, pollen-tube growth and immune responses. Here, we present the cryo-EM structure and electrophysiological analysis of plant CNGC representatives, Arabidopsis CNGC1 and CNGC5. We found that CNGC1 and CNGC5 contain a unique extracellular domain featuring disulfide bonds that is essential for channel gating via coupling of the voltage-sensing domain with the pore domain. The pore domain selectivity filter possesses a Gln residue at the constriction site that determines the Ca selectivity. Replacement of this Gln with Glu, typically observed in CNBD-type non-selective cation channels, could convert CNGC1 and CNGC5 from Ca-selective channels to non-selective cation channels permeable to Ca, Na or K. In addition, we found that the CNGC1 and CNGC5 CNBD homology domain contains intrinsic-ligand-like interactions, which may devoid the binding of cyclic nucleotides and lead to gating independent of cAMP or cGMP. This research not only provides a mechanistic understanding of plant CNGCs' function, but also adds to the comprehensive knowledge of the CNBD channels.
History
DepositionAug 7, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61105.png

Downloads & links

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Map

FileDownload / File: emd_61105.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 360 pix.
= 335.52 Å		0.93 Å/pix.
x 360 pix.
= 335.52 Å		0.93 Å/pix.
x 360 pix.
= 335.52 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.43
Minimum - Maximum-5.4230185 - 7.451859
Average (Standard dev.)-0.0016421812 (±0.108341776)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 335.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61105_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61105_half_map_2.map
Projections & Slices
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Sample components

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Entire : Structure of CNGC1 in GDN

EntireName: Structure of CNGC1 in GDN
Components
  • Complex: Structure of CNGC1 in GDN
    • Protein or peptide: Cyclic nucleotide-gated ion channel 1
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: Structure of CNGC1 in GDN

SupramoleculeName: Structure of CNGC1 in GDN / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Cyclic nucleotide-gated ion channel 1

MacromoleculeName: Cyclic nucleotide-gated ion channel 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 83.203141 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MNFRQEKFVR FQDWKSDKTS SDVEYSGKNE IQTGIFQRTI SSISDKFYRS FESSSARIKL FKRSYKSYSF KEAVSKGIGS THKILDPQG PFLQRWNKIF VLACIIAVSL DPLFFYVPII DDAKKCLGID KKMEITASVL RSFTDVFYVL HIIFQFRTGF I APSSRVFG ...String:
MNFRQEKFVR FQDWKSDKTS SDVEYSGKNE IQTGIFQRTI SSISDKFYRS FESSSARIKL FKRSYKSYSF KEAVSKGIGS THKILDPQG PFLQRWNKIF VLACIIAVSL DPLFFYVPII DDAKKCLGID KKMEITASVL RSFTDVFYVL HIIFQFRTGF I APSSRVFG RGVLVEDKRE IAKRYLSSHF IIDILAVLPL PQMVILIIIP HMRGSSSLNT KNMLKFIVFF QYIPRFIRIY PL YKEVTRT SGILTETAWA GAAFNLFLYM LASHVFGAFW YLFSIERETV CWKQACERNN PPCISKLLYC DPETAGGNAF LNE SCPIQT PNTTLFDFGI FLDALQSGVV ESQDFPQKFF YCFWWGLQNL SSLGQNLKTS TYIWEICFAV FISIAGLVLF SFLI GNMQT YLQSTTTRLE EMRVKRRDAE QWMSHRLLPE NLRKRIRRYE QYKWQETRGV DEENLLSNLP KDLRRDIKRH LCLAL LMRV PMFEKMDEQL LDALCDRLQP VLYTEESYIV REGDPVDEML FIMRGKLLTI TTNGGRTGFL NSEYLGAGDF CGEELL TWA LDPHSSSNLP ISTRTVRALM EVEAFALKAD DLKFVASQFR RLHSKQLRHT FRYYSQQWKT WAACFIQAAW RRYIKKK LE ESLKEEENRL QDALAKEACG SSPSLGATIY ASRFAANILR TIRRSGSVRK PRMPERMPPM LLQKPAEPDF NSDD

UniProtKB: Cyclic nucleotide-gated ion channel 1

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 8 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: FEI FALCON IV (4k 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: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 594717
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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