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- EMDB-32597: Cryo-EM structure of AKT1-AtKC1 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-32597
TitleCryo-EM structure of AKT1-AtKC1
Map data
Sample
  • Complex: Complex of AKT1 and AtKC1
    • Protein or peptide: Potassium channel AKT1
    • Protein or peptide: Potassium channel KAT3
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: POTASSIUM ION
KeywordsVGIC / Plant Channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


root hair elongation / regulation of stomatal closure / response to nematode / response to water deprivation / inward rectifier potassium channel activity / monoatomic ion channel complex / potassium ion import across plasma membrane / voltage-gated potassium channel activity / response to salt stress / potassium ion transmembrane transport ...root hair elongation / regulation of stomatal closure / response to nematode / response to water deprivation / inward rectifier potassium channel activity / monoatomic ion channel complex / potassium ion import across plasma membrane / voltage-gated potassium channel activity / response to salt stress / potassium ion transmembrane transport / potassium ion transport / endoplasmic reticulum / 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 KAT3 / Potassium channel AKT1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsDongliang L / Zijie Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structural basis for the regulation mechanism of a hyper polarization-activated K+ channel AKT1 by AtKC1
Authors: Dongliang L / Zijie Z / Yannan Q / Yuyue T / Huaizong S
History
DepositionJan 14, 2022-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32597.png

Downloads & links

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Map

FileDownload / File: emd_32597.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 240 pix.
= 258.552 Å		1.08 Å/pix.
x 240 pix.
= 258.552 Å		1.08 Å/pix.
x 240 pix.
= 258.552 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0773 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.633
Minimum - Maximum-5.1276813 - 8.034136999999999
Average (Standard dev.)0.012547277 (±0.14360774)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 258.552 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Complex of AKT1 and AtKC1

EntireName: Complex of AKT1 and AtKC1
Components
  • Complex: Complex of AKT1 and AtKC1
    • Protein or peptide: Potassium channel AKT1
    • Protein or peptide: Potassium channel KAT3
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: POTASSIUM ION

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Supramolecule #1: Complex of AKT1 and AtKC1

SupramoleculeName: Complex of AKT1 and AtKC1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Potassium channel AKT1

MacromoleculeName: Potassium channel AKT1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 99.812266 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 LIFATDSLEG SDEVDAGSAA ASGGSGSDYK DDDDK

UniProtKB: Potassium channel AKT1

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Macromolecule #2: Potassium channel KAT3

MacromoleculeName: Potassium channel KAT3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 78.435859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSTTTTEARS PLPLLLRRGR SSTALSASTA EARSPLSILQ FRRRSSKDVR NITSVSSSLL PAFGTFIEDD NPSSKPFIVL HFDRRYRLW ELFLVILVGY SAWASLFELA FEKAAEGALL TIDLVVDFFF AVDIILTFFV SYLDNTTYLN VTDHKLIAKR Y LKSVAFVM ...String:
MSTTTTEARS PLPLLLRRGR SSTALSASTA EARSPLSILQ FRRRSSKDVR NITSVSSSLL PAFGTFIEDD NPSSKPFIVL HFDRRYRLW ELFLVILVGY SAWASLFELA FEKAAEGALL TIDLVVDFFF AVDIILTFFV SYLDNTTYLN VTDHKLIAKR Y LKSVAFVM DVASTLPIQF IYKTITGDVG RGQAFGFLNL LRLWRLRRVA ELFKRLEKDA HFNYFVIRVI KLLCVTIFWI HL AGCILYW IAYHYPRPTD TWIGSQVEDF KERSVWLGYT YSMYWSIVTL TTVGYGDLHA VNSREKTFNM FYMLFNIGLT SYI IGIMTN LVVHGALRTF AMRSAINDIL RYTSKNRLPD TMREQMLAHM QLKFKTAELR QEEVLQDLPK AIRSSINQHL FRSI IEEAY LFKGFPEGLL VQLVSQIQAE YFPPKMEIIL QNEIPTDFYV IVSGGVDIIA SKGVSEQVLA KLGPGSMAGE IGVVF NIPQ PFTVRTRRLS QVIRIGHHKF KEMVQSDNDV DAKMIIANFM TYLKGLNDEL KKEIPFLRDL LDDADAQVQE TVQSEE TPQ SNDEEIVTVS RHENGQIEER RREGVPKRVI IHGQAPPNQD NKNNGDSNGR LIILPDSIQL LFDLAEKKLG KRGSTIA MA DGAHVEQIDA LRENDHLYIF LEGSDEVDAG SAAASGGSGS WSHPQFEK

UniProtKB: Potassium channel KAT3

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Macromolecule #3: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 3 / Number of copies: 4 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #4: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 4 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 289326
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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