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- EMDB-61107: Cryo-EM structure of Arabidopsis CNGC5 -

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Basic information

Entry
Database: EMDB / ID: EMD-61107
TitleCryo-EM structure of Arabidopsis CNGC5
Map data
Sample
  • Complex: Structure of CNGC5 in GDN
    • Protein or peptide: Probable cyclic nucleotide-gated ion channel 5
KeywordsCryo-EM / Membrane protein / polymer / PLANT PROTEIN
Function / homology
Function and homology information


root hair / intracellularly cGMP-activated cation channel activity / cGMP binding / cAMP binding / calcium channel activity / calmodulin binding / plasma membrane
Similarity search - Function
IQ motif profile. / 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
Probable cyclic nucleotide-gated ion channel 5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 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_61107.png

Downloads & links

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Map

FileDownload / File: emd_61107.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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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.47
Minimum - Maximum-3.979629 - 5.9186783
Average (Standard dev.)-0.00031987194 (±0.09903984)
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_61107_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61107_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Structure of CNGC5 in GDN

EntireName: Structure of CNGC5 in GDN
Components
  • Complex: Structure of CNGC5 in GDN
    • Protein or peptide: Probable cyclic nucleotide-gated ion channel 5

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Supramolecule #1: Structure of CNGC5 in GDN

SupramoleculeName: Structure of CNGC5 in GDN / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Probable cyclic nucleotide-gated ion channel 5

MacromoleculeName: Probable cyclic nucleotide-gated ion channel 5 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 83.199812 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MDYKDDDDKM AGKRENFVRV DDLDSRLPSS SVAFQQNYAS NFSGQLHPIH ASNETSRSFK KGIQKGSKGL KSIGRSLGFG VYRAVFPED LKVSEKKIFD PQDKFLLYCN KLFVASCILS VFVDPFFFYL PVINAESKCL GIDRKLAITA STLRTFIDVF Y LAHMALQL ...String:
MDYKDDDDKM AGKRENFVRV DDLDSRLPSS SVAFQQNYAS NFSGQLHPIH ASNETSRSFK KGIQKGSKGL KSIGRSLGFG VYRAVFPED LKVSEKKIFD PQDKFLLYCN KLFVASCILS VFVDPFFFYL PVINAESKCL GIDRKLAITA STLRTFIDVF Y LAHMALQL RTAYIAPSSR VFGRGELVID PAQIAKRYLQ RWFIIDFLSV LPLPQIVVWR FLQSSNGSDV LATKQALLFI VL VQYIPRF LRVLPLTSEL KRTAGVFAET AWAGAAYYLL LYMLASHIVG AFWYLLALER NDACWQEACI DAGNCSTDFL YCG NQNMDG YAVWNRAKES VLKSKCRADL DDNNPPFDFG IYTQALSSGI VSSQNFIVKY CYCLWWGLQN LSTLGQGLET STYP MEIIF SISLAISGLI LFALLIGNMQ TYLQSLTIRL EEMRVKRRDS EQWMHHRMLP QDLRERVRRY DQYKWLETRG VDEEY LVQN LPKDLRRDIK RHLCLALVRR VPLFKSMDDK LLDAICMRLK PCLFTESTYL VREGDPVDEM LFIIRGRLES VTTDGG RSG FFNRSLLKEG EFCGEELLTW ALDPKSGVNL PSSTRTVKAL TEVEAFALTS EELKFVASQF RRLHSRQVQH TFRFYSH QW RTWAACFIQA AWRRYCKRKK MEEAEAEAAA VSSSTAGPSY SIGAAFLATK FAANALRTIH RNRNTKIRDL VKLQKPPE P DFTAD

UniProtKB: Probable cyclic nucleotide-gated ion channel 5

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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: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 204715
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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