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- EMDB-27387: Cryo-EM structure of the zebrafish two pore domain K+ channel TRE... -

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Basic information

Entry
Database: EMDB / ID: EMD-27387
TitleCryo-EM structure of the zebrafish two pore domain K+ channel TREK1 (K2P2.1) in DDM/POPA mixed micelles
Map datadrTREK1 in DDM/POPA mixed micelles full map
Sample
  • Organelle or cellular component: Potassium channel subfamily K member 2
    • Protein or peptide: Potassium channel, subfamily K, member 2a
  • Ligand: (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate
  • Ligand: POTASSIUM IONPotassium
Function / homology:
Function and homology information
Biological speciesDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsSchmidpeter PAM / Nimigean CM / Riegelhaupt PM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K08GM132781 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM145918 United States
CitationJournal: Nat Commun / Year: 2023
Title: Membrane phospholipids control gating of the mechanosensitive potassium leak channel TREK1.
Authors: Philipp A M Schmidpeter / John T Petroff / Leila Khajoueinejad / Aboubacar Wague / Cheryl Frankfater / Wayland W L Cheng / Crina M Nimigean / Paul M Riegelhaupt /
Abstract: Tandem pore domain (K2P) potassium channels modulate resting membrane potentials and shape cellular excitability. For the mechanosensitive subfamily of K2Ps, the composition of phospholipids within ...Tandem pore domain (K2P) potassium channels modulate resting membrane potentials and shape cellular excitability. For the mechanosensitive subfamily of K2Ps, the composition of phospholipids within the bilayer strongly influences channel activity. To examine the molecular details of K2P lipid modulation, we solved cryo-EM structures of the TREK1 K2P channel bound to either the anionic lipid phosphatidic acid (PA) or the zwitterionic lipid phosphatidylethanolamine (PE). At the extracellular face of TREK1, a PA lipid inserts its hydrocarbon tail into a pocket behind the selectivity filter, causing a structural rearrangement that recapitulates mutations and pharmacology known to activate TREK1. At the cytoplasmic face, PA and PE lipids compete to modulate the conformation of the TREK1 TM4 gating helix. Our findings demonstrate two distinct pathways by which anionic lipids enhance TREK1 activity and provide a framework for a model that integrates lipid gating with the effects of other mechanosensitive K2P modulators.
History
DepositionJun 20, 2022-
Header (metadata) releaseMar 8, 2023-
Map releaseMar 8, 2023-
UpdateMar 29, 2023-
Current statusMar 29, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27387.png

Downloads & links

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Map

FileDownload / File: emd_27387.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdrTREK1 in DDM/POPA mixed micelles full map
Voxel sizeX=Y=Z: 1.278 Å
Density
Contour LevelBy AUTHOR: 0.0119
Minimum - Maximum-0.07423248 - 0.11947502
Average (Standard dev.)2.2150166e-06 (±0.0022774972)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 245.376 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27387_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: drTREK1 in DDM/POPA mixed micelles halfmap1

Fileemd_27387_half_map_1.map
AnnotationdrTREK1 in DDM/POPA mixed micelles halfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: drTREK1 in DDM/POPA mixed micelles halfmap2

Fileemd_27387_half_map_2.map
AnnotationdrTREK1 in DDM/POPA mixed micelles halfmap2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Potassium channel subfamily K member 2

EntireName: Potassium channel subfamily K member 2
Components
  • Organelle or cellular component: Potassium channel subfamily K member 2
    • Protein or peptide: Potassium channel, subfamily K, member 2a
  • Ligand: (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate
  • Ligand: POTASSIUM IONPotassium

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Supramolecule #1: Potassium channel subfamily K member 2

SupramoleculeName: Potassium channel subfamily K member 2 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Danio rerio (zebrafish)

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Macromolecule #1: Potassium channel, subfamily K, member 2a

MacromoleculeName: Potassium channel, subfamily K, member 2a / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 35.559383 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 V

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Macromolecule #2: (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec...

MacromoleculeName: (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate
type: ligand / ID: 2 / Number of copies: 4 / Formula: D21
Molecular weightTheoretical: 674.929 Da
Chemical component information

ChemComp-D21:
(2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / 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

Concentration3 mg/mL
BufferpH: 8 / Details: 150mM KCl, 20mM TRIS, 0.25mM DDM, 0.1mg/ml POPA
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec. / Pretreatment - Pressure: 0.03 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
SoftwareName: Leginon
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 63.32 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 492284
Startup modelType of model: NONE / Details: ab-initio model created in RELION
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.2)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 303950
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: UCSF Chimera (ver. 1.14.0)
Details: Model was first docked into density using Chimera Fit in Map tool
Output model

PDB-8de8:
Cryo-EM structure of the zebrafish two pore domain K+ channel TREK1 (K2P2.1) in DDM/POPA mixed micelles

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