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- EMDB-25169: TWIK1 in MSP1E3D1 Lipid Nanodisc at pH 5.5 -

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Basic information

Entry
Database: EMDB / ID: EMD-25169
TitleTWIK1 in MSP1E3D1 Lipid Nanodisc at pH 5.5
Map dataTWIK1 in MSP1E3D1 Lipid Nanodisc at pH 5.5
Sample
  • Complex: TWIK1 in MSPE3D1 Lipid Nanodisc at pH 5.5
    • Protein or peptide: Potassium channel subfamily K member 1
  • Ligand: POTASSIUM ION
  • Ligand: N-OCTANE
  • Ligand: TETRADECANE
KeywordsK+ Channel / pH / TRANSPORT PROTEIN
Function / homology
Function and homology information


Tandem of pore domain in a weak inwardly rectifying K+ channels (TWIK) / Phase 4 - resting membrane potential / potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / inward rectifier potassium channel complex / ligand-gated channel activity / potassium ion leak channel activity / regulation of resting membrane potential / inward rectifier potassium channel activity / cellular response to acidic pH ...Tandem of pore domain in a weak inwardly rectifying K+ channels (TWIK) / Phase 4 - resting membrane potential / potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / inward rectifier potassium channel complex / ligand-gated channel activity / potassium ion leak channel activity / regulation of resting membrane potential / inward rectifier potassium channel activity / cellular response to acidic pH / glutamate secretion / sodium channel activity / potassium channel activity / potassium ion transmembrane transport / sodium ion transmembrane transport / chloride transmembrane transport / synaptic membrane / response to nicotine / brush border membrane / recycling endosome / perikaryon / endosome / apical plasma membrane / protein heterodimerization activity / dendrite / identical protein binding / membrane / plasma membrane
Similarity search - Function
Two pore domain potassium channel, TWIK-1 / Two pore domain potassium channel, TWIK family / Two pore domain potassium channel, TASK family / Two pore domain potassium channel / Potassium channel domain / Ion channel
Similarity search - Domain/homology
Potassium channel subfamily K member 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsTurney TS / Brohawn SG
Funding support United States, 2 items
OrganizationGrant numberCountry
Other private United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM123496 United States
Citation
Journal: Nat Commun / Year: 2022
Title: Structural Basis for pH-gating of the K channel TWIK1 at the selectivity filter.
Authors: Toby S Turney / Vivian Li / Stephen G Brohawn /
Abstract: TWIK1 (K2P1.1, KCNK1) is a widely expressed pH-gated two-pore domain K channel (K2P) that contributes to cardiac rhythm generation and insulin release from pancreatic beta cells. TWIK1 displays ...TWIK1 (K2P1.1, KCNK1) is a widely expressed pH-gated two-pore domain K channel (K2P) that contributes to cardiac rhythm generation and insulin release from pancreatic beta cells. TWIK1 displays unique properties among K2Ps including low basal activity and inhibition by extracellular protons through incompletely understood mechanisms. Here, we present cryo-EM structures of TWIK1 in lipid nanodiscs at high and low pH that reveal a previously undescribed gating mechanism at the K selectivity filter. At high pH, TWIK1 adopts an open conformation. At low pH, protonation of an extracellular histidine results in a cascade of conformational changes that close the channel by sealing the top of the selectivity filter, displacing the helical cap to block extracellular ion access pathways, and opening gaps for lipid block of the intracellular cavity. These data provide a mechanistic understanding for extracellular pH-gating of TWIK1 and illustrate how diverse mechanisms have evolved to gate the selectivity filter of K channels.
#1: Journal: Biorxiv / Year: 2021
Title: Structural Basis for pH-Gating of the K + Channel TWIK1 at the Selectivity Filter
Authors: Turney TS / Li V / Brohawn SG
History
DepositionOct 19, 2021-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7sk1
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

emd_25169.png

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Map

FileDownload / File: emd_25169.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTWIK1 in MSP1E3D1 Lipid Nanodisc at pH 5.5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 200 pix.
= 223. Å		1.12 Å/pix.
x 200 pix.
= 223. Å		1.12 Å/pix.
x 200 pix.
= 223. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.115 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.28535205 - 0.3445472
Average (Standard dev.)0.00009887309 (±0.007828356)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 223.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1151.1151.115
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z223.000223.000223.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.2850.3450.000

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Supplemental data

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Mask #1

Fileemd_25169_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_25169_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_25169_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : TWIK1 in MSPE3D1 Lipid Nanodisc at pH 5.5

EntireName: TWIK1 in MSPE3D1 Lipid Nanodisc at pH 5.5
Components
  • Complex: TWIK1 in MSPE3D1 Lipid Nanodisc at pH 5.5
    • Protein or peptide: Potassium channel subfamily K member 1
  • Ligand: POTASSIUM ION
  • Ligand: N-OCTANE
  • Ligand: TETRADECANE

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Supramolecule #1: TWIK1 in MSPE3D1 Lipid Nanodisc at pH 5.5

SupramoleculeName: TWIK1 in MSPE3D1 Lipid Nanodisc at pH 5.5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Potassium channel subfamily K member 1

MacromoleculeName: Potassium channel subfamily K member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 38.265984 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MLQSLAGSSC VRLVERHRSA WCFGFLVLGY LLYLVFGAVV FSSVELPYED LLRQELRKLK RRFLEEHECL SEPQLEQFLG RVLEASNYG VSVLSNASGN WNWDFTSALF FASTVLSTTG YGHTVPLSDG GKAFCIIYSV IGIPFTLLFL TAVVQRVTVH V TRRPVLYF ...String:
MLQSLAGSSC VRLVERHRSA WCFGFLVLGY LLYLVFGAVV FSSVELPYED LLRQELRKLK RRFLEEHECL SEPQLEQFLG RVLEASNYG VSVLSNASGN WNWDFTSALF FASTVLSTTG YGHTVPLSDG GKAFCIIYSV IGIPFTLLFL TAVVQRVTVH V TRRPVLYF HIRWGFSKQV VAIVHAVLLG FVTVSCFFFI PAAVFSVLED DWNFLESFYF CFISLSTIGL GDYVPGEGYN QK FRELYKI GITCYLLLGL IAMLVVLETF CELHELKKFR KMFYVKKDKD EDQVHIMEHD QLSFSSITEQ AAGLKEEQKQ NEP FVASQS PPYEDGSANH

UniProtKB: Potassium channel subfamily K member 1

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #3: N-OCTANE

MacromoleculeName: N-OCTANE / type: ligand / ID: 3 / Number of copies: 2 / Formula: OCT
Molecular weightTheoretical: 114.229 Da
Chemical component information

ChemComp-OCT:
N-OCTANE

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Macromolecule #4: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 4 / Number of copies: 2 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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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: 5.5
Component:
ConcentrationFormulaName
20.0 mMC6H13NO4SMES
150.0 mMKClPotassium Chloride
1.0 mMC10H16N2O8EDTA
GridModel: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.3523 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3ukm

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 38126
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3ukm


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 143 / Target criteria: Correlation coefficient
Output model

PDB-7sk1:
TWIK1 in MSP1E3D1 Lipid Nanodisc at pH 5.5

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