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- EMDB-46725: Danio rerio TREK-1:CBD complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-46725
TitleDanio rerio TREK-1:CBD complex
Map datasharpened map
Sample
  • Complex: TREK-1 homodimer
    • Protein or peptide: Potassium channel subfamily K member 2
  • Ligand: POTASSIUM ION
  • Ligand: cannabidiol
KeywordsION CHANNEL / K2P / K2P2.1 / TREK1 / TREK-1 / CANNABINOID / MEMBRANE PROTEIN
Function / homology
Function and homology information


potassium ion leak channel activity / mechanosensitive monoatomic ion channel activity / outward rectifier potassium channel activity / potassium ion transmembrane transport / plasma membrane
Similarity search - Function
Two pore domain potassium channel, TREK / Two pore domain potassium channel / Potassium channel domain / Ion channel
Similarity search - Domain/homology
Potassium channel subfamily K member 2 isoform X1
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsDocter T / Brohawn SG
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM145869 United States
CitationJournal: To Be Published
Title: Cannabinoid inhibition of mechanosensitive K+ channels
Authors: Docter T / Sorum B / Deshmane R / Doubvravsky C / Brohawn SG
History
DepositionAug 23, 2024-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46725.png

Downloads & links

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Map

FileDownload / File: emd_46725.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 300 pix.
= 254.4 Å		0.85 Å/pix.
x 300 pix.
= 254.4 Å		0.85 Å/pix.
x 300 pix.
= 254.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.848 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.22911061 - 0.3022475
Average (Standard dev.)0.00013572651 (±0.006028116)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 254.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_46725_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_46725_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_46725_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TREK-1 homodimer

EntireName: TREK-1 homodimer
Components
  • Complex: TREK-1 homodimer
    • Protein or peptide: Potassium channel subfamily K member 2
  • Ligand: POTASSIUM ION
  • Ligand: cannabidiol

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Supramolecule #1: TREK-1 homodimer

SupramoleculeName: TREK-1 homodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 73 KDa

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Macromolecule #1: Potassium channel subfamily K member 2

MacromoleculeName: Potassium channel subfamily K member 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 36.664578 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MAAPDLLDPK SATHNTKPRL SFSSKPIVYN SGDDCESITT VMKWKTVLAI FLLVVLYLII GATVFKALEQ PEEGLQKYRI IQEKIDFLS MHTCVQTSEL EDLVKQVVLA IRAGVNPSGH PSQESSMWDL SSSFFFAGTV ITTIGFGNVS PHTEGGRIFC I IYALLGIP ...String:
MAAPDLLDPK SATHNTKPRL SFSSKPIVYN SGDDCESITT VMKWKTVLAI FLLVVLYLII GATVFKALEQ PEEGLQKYRI IQEKIDFLS MHTCVQTSEL EDLVKQVVLA IRAGVNPSGH PSQESSMWDL SSSFFFAGTV ITTIGFGNVS PHTEGGRIFC I IYALLGIP LFGFLLAGVG DQLGTIFGKG IAKVEKMFVK WNVSQTKIRV TSTVLFILFG CLLFVALPAL IFQHIEGWSA LE SIYFVVI TLTTIGFGDF VAGGSEIEYL DYYKPIVWFW ILVGLAYFAA VLSMIGDWLR VISKKTKEEV GEFRAHAAEW TAN VSSNSL EVLFQ

UniProtKB: Potassium channel subfamily K member 2 isoform X1

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Macromolecule #2: POTASSIUM ION

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

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Macromolecule #3: cannabidiol

MacromoleculeName: cannabidiol / type: ligand / ID: 3 / Number of copies: 1 / Formula: P0T
Molecular weightTheoretical: 314.462 Da
Chemical component information

ChemComp-P0T:
cannabidiol

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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

Concentration4.4 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3TRIS
150.0 mMKClPotassium chloride
1.0 mMC10H16N2O8Ethylene diamine tetraacetic acid
0.5 mMC24H46O11Dodecyl maltoside
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8de7

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 117609
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)

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