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- EMDB-61063: Cryo-EM Structure of the Guard Cell Potassium Channel GORK N50 de... -

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Basic information

Entry
Database: EMDB / ID: EMD-61063
TitleCryo-EM Structure of the Guard Cell Potassium Channel GORK N50 deletion
Map data
Sample
  • Complex: GORK N50 deletion
    • Protein or peptide: Potassium channel GORK
  • Ligand: POTASSIUM ION
KeywordsGuard cell / Potassium channel / outward-rectifying / MEMBRANE PROTEIN
Function / homology
Function and homology information


monoatomic ion transmembrane transporter activity / response to jasmonic acid / response to water deprivation / response to abscisic acid / outward rectifier potassium channel activity / monoatomic ion channel complex / monoatomic ion transport / response to cold / response to calcium ion / nucleus
Similarity search - Function
Potassium channel KAT/AKT / KHA domain / KHA, dimerisation domain of potassium ion channel / KHA domain profile. / 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 ...Potassium channel KAT/AKT / KHA domain / KHA, dimerisation domain of potassium ion channel / KHA domain profile. / 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 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Potassium channel GORK
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsZhang X / Zhang P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: GORK K channel structure and gating vital to informing stomatal engineering.
Authors: Xue Zhang / William Carroll / Thu Binh-Anh Nguyen / Thanh-Hao Nguyen / Zhao Yang / Miaolian Ma / Xiaowei Huang / Adrian Hills / Hui Guo / Rucha Karnik / Michael R Blatt / Peng Zhang /
Abstract: The Arabidopsis GORK channel is a major pathway for guard cell K efflux that facilitates stomatal closure. GORK is an outwardly-rectifying member of the cyclic-nucleotide binding-homology domain ...The Arabidopsis GORK channel is a major pathway for guard cell K efflux that facilitates stomatal closure. GORK is an outwardly-rectifying member of the cyclic-nucleotide binding-homology domain (CNBHD) family of K channels with close homologues in all other angiosperms known to date. Its bioengineering has demonstrated the potential for enhanced carbon assimilation and water use efficiency. Here we identify critical domains through structural and functional analysis, highlighting conformations that reflect long-lived closed and pre-open states of GORK. These conformations are marked by interactions at the cytosolic face of the membrane between so-called voltage-sensor, C-linker and CNBHD domains, the latter relocating across 10 Å below the voltage sensor. The interactions center around two coupling sites that functional analysis establish are critical for channel gating. The channel is also subject to putative, ligand-like interactions within the CNBHD, which leads to its gating independence of cyclic nucleotides such as cAMP or cGMP. These findings implicate a multi-step mechanism of semi-independent conformational transitions that underlie channel activity and offer promising new sites for optimizing GORK to engineer stomata.
History
DepositionAug 3, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61063.png

Downloads & links

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Map

FileDownload / File: emd_61063.map.gz / Format: CCP4 / Size: 371.3 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 460 pix.
= 428.72 Å		0.93 Å/pix.
x 460 pix.
= 428.72 Å		0.93 Å/pix.
x 460 pix.
= 428.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.26
Minimum - Maximum-1.6148605 - 3.0694933
Average (Standard dev.)-0.00019045705 (±0.04834075)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 428.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpen map

Fileemd_61063_additional_1.map
Annotationunsharpen map
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Half map: #2

Fileemd_61063_half_map_1.map
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Half map: #1

Fileemd_61063_half_map_2.map
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Sample components

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Entire : GORK N50 deletion

EntireName: GORK N50 deletion
Components
  • Complex: GORK N50 deletion
    • Protein or peptide: Potassium channel GORK
  • Ligand: POTASSIUM ION

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Supramolecule #1: GORK N50 deletion

SupramoleculeName: GORK N50 deletion / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Potassium channel GORK

MacromoleculeName: Potassium channel GORK / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 88.589945 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HNDYKYIIHP KNRWYKAWEM FILVWAIYSS LFTPMEFGFF RGLPERLFVL DIVGQIAFLV DIVLQFFVAY RDTQTYRTVY KPTRIAFRY LKSHFLMDFI GCFPWDLIYK ASGKHELVRY LLWIRLFRVR KVVEFFQRLE KDTRINYLFT RILKLLFVEV Y CTHTAACI ...String:
HNDYKYIIHP KNRWYKAWEM FILVWAIYSS LFTPMEFGFF RGLPERLFVL DIVGQIAFLV DIVLQFFVAY RDTQTYRTVY KPTRIAFRY LKSHFLMDFI GCFPWDLIYK ASGKHELVRY LLWIRLFRVR KVVEFFQRLE KDTRINYLFT RILKLLFVEV Y CTHTAACI FYYLATTLPP ENEGYTWIGS LKLGDYSYEN FREIDLWKRY TTALYFAIVT MATVGYGDIH AVNLREMIFV MI YVSFDMV LGAYLIGNIT ALIVKGSNTE RFRDKMNDLI SFMNRKKLGR DLRSQITGHV RLQYDSHYTD TVMLQDIPAS IRA KIAQLL YLPYIKKVPL FKGCSTEFIN QIVIRLHEEY FLPGEVITEQ GNVVDHLYFV CEGLLEALVT KTDGSEESVT LLGP HTSFG DISIICNISQ PFTVRVCELC HLLRLDKQSF SNILEIYFHD GRTILNNIME EKESNDRIKK LESDIVIHIG KQEAE LALK VNSAAFQGDF YQLKSLIRSG ADPNKTDYDG RSPLHLAACR GYEDITLFLI QEGVDVNLKD KFGHTPLFEA VKAGQE GVI GLLVKEGASF NLEDSGNFLC TTVAKGDSDF LKRLLSSGMN PNSEDYDHRT PLHVAASEGL FLMAKMLVEA GASVISK DR WGNSPLDEAR LCGNKKLIKL LEDVKNAQSS IYPSSLRELQ EERIERRKCT VFPFHPQEAK EERSRKHGVV VWIPSNLE K LIVTAAKELG LSDGASFVLL SEDQGRITDI DMISDGHKLY MISDTTDQT

UniProtKB: Potassium channel GORK

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 152349
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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