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- EMDB-62921: Arabidopsis GORK consensus structure -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-62921
TitleArabidopsis GORK consensus structure
Map data
Sample
  • Complex: GORK
    • Protein or peptide: Potassium channel GORK
KeywordsOutward potassium channel in stomata / PLANT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsYamanashi T / Kume T / Sekido N / Muraoka Y / Yokoyama T / Tanaka Y / Uozumi N
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: To Be Published
Title: Structure Reveals Regulation Mechanism of Plant Outward-Rectifying K+ channel GORK by Structural Rearrangements in CNBD-Ankyrin-bridge
Authors: Yamanashi T / Muraoka Y / Furuta T / Kume T / Sekido N / Saito S / Terashima S / Yokoyama T / Tanaka Y / Miyamoto A / Sato K / Ito T / Nakazawa H / Umetsu M / Tanudjaja E / Tsujii M / Dreyer ...Authors: Yamanashi T / Muraoka Y / Furuta T / Kume T / Sekido N / Saito S / Terashima S / Yokoyama T / Tanaka Y / Miyamoto A / Sato K / Ito T / Nakazawa H / Umetsu M / Tanudjaja E / Tsujii M / Dreyer I / Schroeder JI / Ishimaru Y / Uozumi N
History
DepositionJan 1, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62921.png

Downloads & links

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Map

FileDownload / File: emd_62921.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 400 pix.
= 315.2 Å		0.79 Å/pix.
x 400 pix.
= 315.2 Å		0.79 Å/pix.
x 400 pix.
= 315.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.788 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-1.0532 - 1.6707766
Average (Standard dev.)0.00047435606 (±0.028901648)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 315.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62921_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_62921_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GORK

EntireName: GORK
Components
  • Complex: GORK
    • Protein or peptide: Potassium channel GORK

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Supramolecule #1: GORK

SupramoleculeName: GORK / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: 96.409344 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDYKDDDDKG RLRRRQEIID HEEEESNDDV SSRRGKLSLA ETFRWLDSSE HRRIETDGHN DYKYIIHPKN RWYKAWEMFI LVWAIYSSL FTPMEFGFFR GLPERLFVLD IVGQIAFLVD IVLQFFVAYR DTQTYRTVYK PTRIAFRYLK SHFLMDFIGC F PWDLIYKA ...String:
MDYKDDDDKG RLRRRQEIID HEEEESNDDV SSRRGKLSLA ETFRWLDSSE HRRIETDGHN DYKYIIHPKN RWYKAWEMFI LVWAIYSSL FTPMEFGFFR GLPERLFVLD IVGQIAFLVD IVLQFFVAYR DTQTYRTVYK PTRIAFRYLK SHFLMDFIGC F PWDLIYKA SGKHELVRYL LWIRLFRVRK VVEFFQRLEK DTRINYLFTR ILKLLFVEVY CTHTAACIFY YLATTLPPEN EG YTWIGSL KLGDYSYENF REIDLWKRYT TALYFAIVTM ATVGYGDIHA VNLREMIFVM IYVSFDMVLG AYLIGNITAL IVK GSNTER FRDKMNDLIS FMNRKKLGRD LRSQITGHVR LQYDSHYTDT VMLQDIPASI RAKIAQLLYL PYIKKVPLFK GCST EFINQ IVIRLHEEYF LPGEVITEQG NVVDHLYFVC EGLLEALVTK TDGSEESVTL LGPHTSFGDI SIICNISQPF TVRVC ELCH LLRLDKQSFS NILEIYFHDG RTILNNIMEE KESNDRIKKL ESDIVIHIGK QEAELALKVN SAAFQGDFYQ LKSLIR SGA DPNKTDYDGR SPLHLAACRG YEDITLFLIQ EGVDVNLKDK FGHTPLFEAV KAGQEGVIGL LVKEGASFNL EDSGNFL CT TVAKGDSDFL KRLLSSGMNP NSEDYDHRTP LHVAASEGLF LMAKMLVEAG ASVISKDRWG NSPLDEARLC GNKKLIKL L EDVKNAQSSI YPSSLRELQE ERIERRKCTV FPFHPQEAKE ERSRKHGVVV WIPSNLEKLI VTAAKELGLS DGASFVLLS EDQGRITDID MISDGHKLYM ISDTTDQTHH HHHH

UniProtKB: Potassium channel GORK

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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

Concentration4.0 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 206532
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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