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- EMDB-21843: TASK2 in MSP1D1 lipid nanodisc at pH 6.5 -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-21843
TitleTASK2 in MSP1D1 lipid nanodisc at pH 6.5
Map datapH 6.5
Sample
  • Complex: TASK2 in MSP1D1 lipid nanodisc at pH 6.5
    • Protein or peptide: Potassium channel TASK2
  • Ligand: POTASSIUM IONPotassium
Function / homology
Function and homology information


Phase 4 - resting membrane potential / stabilization of membrane potential / potassium ion export across plasma membrane / regulation of resting membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / potassium ion import across plasma membrane / voltage-gated potassium channel activity / potassium channel activity / potassium ion transmembrane transport ...Phase 4 - resting membrane potential / stabilization of membrane potential / potassium ion export across plasma membrane / regulation of resting membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / potassium ion import across plasma membrane / voltage-gated potassium channel activity / potassium channel activity / potassium ion transmembrane transport / potassium ion transport / plasma membrane
Similarity search - Function
Two pore domain potassium channel, TASK family / Two pore domain potassium channel / Potassium channel domain / Ion channel
Similarity search - Domain/homology
Potassium channel TASK2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsLi B / Brohawn SG
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM123496 United States
CitationJournal: Nature / Year: 2020
Title: Structural basis for pH gating of the two-pore domain K channel TASK2.
Authors: Baobin Li / Robert A Rietmeijer / Stephen G Brohawn /
Abstract: TASK2 (also known as KCNK5) channels generate pH-gated leak-type K currents to control cellular electrical excitability. TASK2 is involved in the regulation of breathing by chemosensory neurons of ...TASK2 (also known as KCNK5) channels generate pH-gated leak-type K currents to control cellular electrical excitability. TASK2 is involved in the regulation of breathing by chemosensory neurons of the retrotrapezoid nucleus in the brainstem and pH homeostasis by kidney proximal tubule cells. These roles depend on channel activation by intracellular and extracellular alkalization, but the mechanistic basis for TASK2 gating by pH is unknown. Here we present cryo-electron microscopy structures of Mus musculus TASK2 in lipid nanodiscs in open and closed conformations. We identify two gates, distinct from previously observed K channel gates, controlled by stimuli on either side of the membrane. Intracellular gating involves lysine protonation on inner helices and the formation of a protein seal between the cytoplasm and the channel. Extracellular gating involves arginine protonation on the channel surface and correlated conformational changes that displace the K-selectivity filter to render it nonconductive. These results explain how internal and external protons control intracellular and selectivity filter gates to modulate TASK2 activity.
History
DepositionApr 20, 2020-
Header (metadata) releaseJul 15, 2020-
Map releaseJul 15, 2020-
UpdateOct 28, 2020-
Current statusOct 28, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wlv
  • Surface level: 6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21843.png

Downloads & links

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Map

FileDownload / File: emd_21843.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationpH 6.5
Voxel sizeX=Y=Z: 1.137 Å
Density
Contour LevelBy AUTHOR: 6 / Movie #1: 6
Minimum - Maximum-15.184793 - 33.528057
Average (Standard dev.)0.0000000000 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 181.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1371.1371.137
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z181.920181.920181.920
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ160160160
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-15.18533.5280.000

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Supplemental data

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Sample components

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Entire : TASK2 in MSP1D1 lipid nanodisc at pH 6.5

EntireName: TASK2 in MSP1D1 lipid nanodisc at pH 6.5
Components
  • Complex: TASK2 in MSP1D1 lipid nanodisc at pH 6.5
    • Protein or peptide: Potassium channel TASK2
  • Ligand: POTASSIUM IONPotassium

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Supramolecule #1: TASK2 in MSP1D1 lipid nanodisc at pH 6.5

SupramoleculeName: TASK2 in MSP1D1 lipid nanodisc at pH 6.5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Komagataella pastoris (fungus)
Molecular weightTheoretical: 77 KDa

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Macromolecule #1: Potassium channel TASK2

MacromoleculeName: Potassium channel TASK2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 38.533703 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MVDRGPLLTS AIIFYLAIGA AIFEVLEEPH WKEAKKNYYT QKLHLLKEFP CLSQEGLDKI LQVVSDAADQ GVAITGNQTF NNWNWPNAM IFAATVITTI GYGNVAPKTP AGRLFCVFYG LFGVPLCLTW ISALGKFFGG RAKRLGQFLT RRGVSLRKAQ I TCTAIFIV ...String:
MVDRGPLLTS AIIFYLAIGA AIFEVLEEPH WKEAKKNYYT QKLHLLKEFP CLSQEGLDKI LQVVSDAADQ GVAITGNQTF NNWNWPNAM IFAATVITTI GYGNVAPKTP AGRLFCVFYG LFGVPLCLTW ISALGKFFGG RAKRLGQFLT RRGVSLRKAQ I TCTAIFIV WGVLVHLVIP PFVFMVTEEW NYIEGLYYSF ITISTIGFGD FVAGVNPSAN YHALYRYFVE LWIYLGLAWL SL FVNWKVS MFVEVHKAIK KRRRRRKESF ESSPHSRKAL QMAGSTASKD VNIFSFLSKK EETYNDLIKQ IGKKAMKTSG GGE RVPGPG HGLGPQGDRS NSLEVLF

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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.2 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormulaName
20.0 mMKPO4potassium phosphate
150.0 mMKClpotassium chloride
1.0 mMEDTAEthylenediaminetetraacetic acidethylene diamine tetraacetic acid
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Incubate 5 seconds, blot 3s seconds, blot force 1.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 1 / Number real images: 2683 / Average exposure time: 0.11 sec. / Average electron dose: 0.98714 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3563337
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: OTHER / Details: ab initio model from cryosparc 2
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1 beta)
Final 3D classificationSoftware - Name: RELION (ver. 3.1 beta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1 beta)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1 beta) / Number images used: 255808

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 151.61
Output model

PDB-6wlv:
TASK2 in MSP1D1 lipid nanodisc at pH 6.5

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