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- PDB-9l9u: Arabidopsis GORK WT1 -

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Basic information

Entry
Database: PDB / ID: 9l9u
TitleArabidopsis GORK WT1
ComponentsPotassium channel GORK
KeywordsPLANT PROTEIN / Outward potassium channel in stomata
Function / homology
Function and homology information


monoatomic ion transmembrane transporter activity / response to jasmonic acid / response to abscisic acid / response to water deprivation / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsYamanashi, T. / Kume, T. / Sekido, N. / Muraoka, Y. / Yokoyama, T. / Tanaka, Y. / Uozumi, N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structure reveals a regulation mechanism of plant outward-rectifying K channel GORK by structural rearrangements in the CNBD-Ankyrin bridge.
Authors: Taro Yamanashi / Yuki Muraoka / Tadaomi Furuta / Tsukasa Kume / Natsuko Sekido / Shunya Saito / Shota Terashima / Takeshi Yokoyama / Yoshikazu Tanaka / Atsushi Miyamoto / Kanane Sato / ...Authors: Taro Yamanashi / Yuki Muraoka / Tadaomi Furuta / Tsukasa Kume / Natsuko Sekido / Shunya Saito / Shota Terashima / Takeshi Yokoyama / Yoshikazu Tanaka / Atsushi Miyamoto / Kanane Sato / Tomoyuki Ito / Hikaru Nakazawa / Mitsuo Umetsu / Ellen Tanudjaja / Masaru Tsujii / Ingo Dreyer / Julian I Schroeder / Yasuhiro Ishimaru / Nobuyuki Uozumi /
Abstract: Guard cells, which regulate stomatal apertures in plants, possess a sophisticated mechanism for regulating turgor pressure. The outward-rectifying "K" channel GORK, expressed in guard cells of the ...Guard cells, which regulate stomatal apertures in plants, possess a sophisticated mechanism for regulating turgor pressure. The outward-rectifying "K" channel GORK, expressed in guard cells of the plant , is a central component that promotes stomatal closure by releasing K to the extracellular space, thereby lowering turgor pressure. To date, the structural basis underlying the regulation of the K transport activity of GORK is unclear. Using cryo-EM, we determined the structures of the GORK outward-rectifying K channel with a resolution of 3.16 to 3.27 Å in five distinct conformations that differ significantly in their C-terminal cyclic nucleotide binding domain (CNBD) and ankyrin repeat (ANK) domain. The C-linker connects the transmembrane domains to the C-terminal domains, i.e., CNBD, CNBD-Ankyrin bridge, and ANK. The structural changes and interactions in the C-linker determine whether the closed state of GORK is closer to the preopen state or in a more removed state from the open state of the channel. In particular, interconversion in the short sequence within the CNBD-Ankyrin bridge plays a decisive role in this determination. This region forms an α-helix in the preopened state, while it adopts a nonhelical structure in further distant closed states. The dynamics of the cytosolic region strongly suggest that the K channel activity of GORK is regulated by cytosolic signaling factors during stomatal closure.
History
DepositionDec 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium channel GORK
B: Potassium channel GORK
C: Potassium channel GORK
D: Potassium channel GORK


Theoretical massNumber of molelcules
Total (without water)385,6374
Polymers385,6374
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
Potassium channel GORK / Guard cell outward rectifying K(+) channel / AtGORK


Mass: 96409.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GORK, At5g37500, MPA22.4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q94A76
Has protein modificationN

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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: GORK / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26135 / Symmetry type: POINT
RefinementHighest resolution: 3.12 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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