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- EMDB-25691: AKT1 K+ channel from A. thaliana in MSP2N2 lipid nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-25691
TitleAKT1 K+ channel from A. thaliana in MSP2N2 lipid nanodisc
Map dataSharpened electrostatic potential map from cryoSPARC non-uniform refinement.
Sample
  • Complex: Homotetramer of AKT1 subunits
    • Protein or peptide: Potassium channel AKT1
  • Ligand: POTASSIUM ION
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: water
KeywordsK+ channel / ion channel / hyperpolarization-activated channel / voltage-gated channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


root hair elongation / regulation of stomatal closure / response to water deprivation / inward rectifier potassium channel activity / monoatomic ion channel complex / potassium ion import across plasma membrane / response to salt stress / potassium ion transport / identical protein binding / plasma membrane
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 AKT1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsDickinson MS / Pourmal S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM24485 United States
CitationJournal: Biochemistry / Year: 2022
Title: Symmetry Reduction in a Hyperpolarization-Activated Homotetrameric Ion Channel.
Authors: Miles Sasha Dickinson / Sergei Pourmal / Meghna Gupta / Maxine Bi / Robert M Stroud /
Abstract: Plants obtain nutrients from the soil via transmembrane transporters and channels in their root hairs, from which ions radially transport in toward the xylem for distribution across the plant body. ...Plants obtain nutrients from the soil via transmembrane transporters and channels in their root hairs, from which ions radially transport in toward the xylem for distribution across the plant body. We determined structures of the hyperpolarization-activated channel AKT1 from , which mediates K uptake from the soil into plant roots. These structures of AtAKT1 embedded in lipid nanodiscs show that the channel undergoes a reduction of C4 to C2 symmetry, possibly to regulate its electrical activation.
History
DepositionDec 10, 2021-
Header (metadata) releaseDec 22, 2021-
Map releaseDec 22, 2021-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7t4x
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25691.png

Downloads & links

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Map

FileDownload / File: emd_25691.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened electrostatic potential map from cryoSPARC non-uniform refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 432 pix.
= 360.72 Å		0.84 Å/pix.
x 432 pix.
= 360.72 Å		0.84 Å/pix.
x 432 pix.
= 360.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.621 / Movie #1: 0.5
Minimum - Maximum-2.161066 - 4.3646026
Average (Standard dev.)0.0037513464 (±0.07005819)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 360.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8350.8350.835
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z360.720360.720360.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-2.1614.3650.004

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Supplemental data

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Additional map: Density modification using DeepEmhancer. Inputs are two half...

Fileemd_25691_additional_1.map
AnnotationDensity modification using DeepEmhancer. Inputs are two half maps from cryoSPARC non-uniform refinement, using the "high resolution" protocol.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Density modification using phenix.resolve cryo em. Input is two half...

Fileemd_25691_additional_2.map
AnnotationDensity modification using phenix.resolve_cryo_em. Input is two half maps from C4-symmetrized non-uniform refinement (cryoSPARC).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 from cryoSPARC non-uniform refinement

Fileemd_25691_half_map_1.map
AnnotationHalf map 1 from cryoSPARC non-uniform refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 from cryoSPARC non-uniform refinement

Fileemd_25691_half_map_2.map
AnnotationHalf map 2 from cryoSPARC non-uniform refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homotetramer of AKT1 subunits

EntireName: Homotetramer of AKT1 subunits
Components
  • Complex: Homotetramer of AKT1 subunits
    • Protein or peptide: Potassium channel AKT1
  • Ligand: POTASSIUM ION
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: water

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Supramolecule #1: Homotetramer of AKT1 subunits

SupramoleculeName: Homotetramer of AKT1 subunits / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 969.89 KDa

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Macromolecule #1: Potassium channel AKT1

MacromoleculeName: Potassium channel AKT1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 97.109625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRGGALLCGQ VQDEIEQLSR ESSHFSLSTG ILPSLGARSN RRVKLRRFVV SPYDHKYRIW EAFLVVLVVY TAWVSPFEFG FLRKPRPPL SITDNIVNAF FAIDIIMTFF VGYLDKSTYL IVDDRKQIAF KYLRSWFLLD LVSTIPSEAA MRISSQSYGL F NMLRLWRL ...String:
MRGGALLCGQ VQDEIEQLSR ESSHFSLSTG ILPSLGARSN RRVKLRRFVV SPYDHKYRIW EAFLVVLVVY TAWVSPFEFG FLRKPRPPL SITDNIVNAF FAIDIIMTFF VGYLDKSTYL IVDDRKQIAF KYLRSWFLLD LVSTIPSEAA MRISSQSYGL F NMLRLWRL RRVGALFARL EKDRNFNYFW VRCAKLVCVT LFAVHCAACF YYLIAARNSN PAKTWIGANV ANFLEESLWM RY VTSMYWS ITTLTTVGYG DLHPVNTKEM IFDIFYMLFN LGLTAYLIGN MTNLVVHGTS RTRNFRDTIQ AASNFAHRNH LPP RLQDQM LAHLCLKYRT DSEGLQQQET LDALPKAIRS SISHFLFYSL MDKVYLFRGV SNDLLFQLVS EMKAEYFPPK EDVI LQNEA PTDFYILVNG TADLVDVDTG TESIVREVKA GDIIGEIGVL CYRPQLFTVR TKRLCQLLRM NRTTFLNIIQ ANVGD GTII MNNLLQHLKE MNDPVMTNVL LEIENMLARG KMDLPLNLCF AAIREDDLLL HQLLKRGLDP NESDNNGRTP LHIAAS KGT LNCVLLLLEY HADPNCRDAE GSVPLWEAMV EGHEKVVKVL LEHGSTIDAG DVGHFACTAA EQGNLKLLKE IVLHGGD VT RPRATGTSAL HTAVCEENIE MVKYLLEQGA DVNKQDMHGW TPRDLAEQQG HEDIKALFRE KLHERRVHIE TSSSVPIL K TGIRFLGRFT SEPNIRPASR EVSFRIRETR ARRKTNNFDN SLFGILANQS VPKNGLATVD EGRTGNPVRV TISCAEKDD IAGKLVLLPG SFKELLELGS NKFGIVATKV MNKDNNAEID DVDVIRDGDH LIFATDS

UniProtKB: Potassium channel AKT1

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 5 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #3: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 13 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
200.0 mMKClpotassium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsHomotetramer of AKT1 subunits in MSP2N2 lipid nanodisc

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 4660 / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1487609
Startup modelType of model: OTHER / Details: Stochastic gradient descent from particle images
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 81658
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING

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