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- EMDB-32296: CryoEM structure of human Kv4.3 -

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Basic information

Entry
Database: EMDB / ID: EMD-32296
TitleCryoEM structure of human Kv4.3
Map data
Sample
  • Organelle or cellular component: voltage-gated potassium channel Kv4.3
    • Protein or peptide: Isoform 2 of Potassium voltage-gated channel subfamily D member 3
KeywordsPotassium voltage-gated channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


ventricular cardiac muscle cell membrane repolarization / Kv4.3-KChIP1 channel complex / A-type (transient outward) potassium channel activity / Phase 1 - inactivation of fast Na+ channels / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during ventricular cardiac muscle cell action potential / membrane repolarization during cardiac muscle cell action potential / potassium ion export across plasma membrane / membrane repolarization / Voltage gated Potassium channels ...ventricular cardiac muscle cell membrane repolarization / Kv4.3-KChIP1 channel complex / A-type (transient outward) potassium channel activity / Phase 1 - inactivation of fast Na+ channels / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during ventricular cardiac muscle cell action potential / membrane repolarization during cardiac muscle cell action potential / potassium ion export across plasma membrane / membrane repolarization / Voltage gated Potassium channels / postsynaptic specialization membrane / regulation of heart contraction / regulation of heart rate by cardiac conduction / action potential / muscle contraction / voltage-gated potassium channel complex / potassium ion transmembrane transport / GABA-ergic synapse / protein tetramerization / potassium ion transport / sarcolemma / protein homooligomerization / chemical synaptic transmission / dendritic spine / postsynaptic membrane / neuronal cell body / metal ion binding / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, Kv4.3 / Potassium channel, voltage dependent, Kv4 / Potassium channel, voltage dependent, Kv4, C-terminal / Domain of unknown function (DUF3399) / Shal-type voltage-gated potassium channels, N-terminal / Shal-type voltage-gated potassium channels, N-terminal / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel ...Potassium channel, voltage dependent, Kv4.3 / Potassium channel, voltage dependent, Kv4 / Potassium channel, voltage dependent, Kv4, C-terminal / Domain of unknown function (DUF3399) / Shal-type voltage-gated potassium channels, N-terminal / Shal-type voltage-gated potassium channels, N-terminal / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily / SKP1/BTB/POZ domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
A-type voltage-gated potassium channel KCND3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsMa DM / Guo JT
Funding support China, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021FZZX001-28 China
Ministry of Science and Technology (MoST, China)LD21H020001 China
National Natural Science Foundation of China (NSFC)LR19C050002 China
National Natural Science Foundation of China (NSFC)LY19H020007 China
CitationJournal: Cell Res / Year: 2022
Title: Structural basis for the gating modulation of Kv4.3 by auxiliary subunits.
Authors: Demin Ma / Cheng Zhao / Xiaochen Wang / Xiaoxiao Li / Yi Zha / Yan Zhang / Guosheng Fu / Ping Liang / Jiangtao Guo / Dongwu Lai /
History
DepositionNov 26, 2021-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32296.png

Downloads & links

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Map

FileDownload / File: emd_32296.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 270 pix.
= 273.78 Å		1.01 Å/pix.
x 270 pix.
= 273.78 Å		1.01 Å/pix.
x 270 pix.
= 273.78 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0122
Minimum - Maximum-0.036416616 - 0.085047126
Average (Standard dev.)-0.000022821021 (±0.0020850517)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 273.78003 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : voltage-gated potassium channel Kv4.3

EntireName: voltage-gated potassium channel Kv4.3
Components
  • Organelle or cellular component: voltage-gated potassium channel Kv4.3
    • Protein or peptide: Isoform 2 of Potassium voltage-gated channel subfamily D member 3

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Supramolecule #1: voltage-gated potassium channel Kv4.3

SupramoleculeName: voltage-gated potassium channel Kv4.3 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 2 of Potassium voltage-gated channel subfamily D member 3

MacromoleculeName: Isoform 2 of Potassium voltage-gated channel subfamily D member 3
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73.159578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAGVAAWLP FARAAAIGWM PVANCPMPLA PADKNKRQDE LIVLNVSGRR FQTWRTTLER YPDTLLGSTE KEFFFNEDTK EYFFDRDPE VFRCVLNFYR TGKLHYPRYE CISAYDDELA FYGILPEIIG DCCYEEYKDR KRENAERLMD DNDSENNQES M PSLSFRQT ...String:
MAAGVAAWLP FARAAAIGWM PVANCPMPLA PADKNKRQDE LIVLNVSGRR FQTWRTTLER YPDTLLGSTE KEFFFNEDTK EYFFDRDPE VFRCVLNFYR TGKLHYPRYE CISAYDDELA FYGILPEIIG DCCYEEYKDR KRENAERLMD DNDSENNQES M PSLSFRQT MWRAFENPHT STLALVFYYV TGFFIAVSVI TNVVETVPCG TVPGSKELPC GERYSVAFFC LDTACVMIFT VE YLLRLFA APSRYRFIRS VMSIIDVVAI MPYYIGLVMT NNEDVSGAFV TLRVFRVFRI FKFSRHSQGL RILGYTLKSC ASE LGFLLF SLTMAIIIFA TVMFYAEKGS SASKFTSIPA SFWYTIVTMT TLGYGDMVPK TIAGKIFGSI CSLSGVLVIA LPVP VIVSN FSRIYHQNQR ADKRRAQKKA RLARIRVAKT GSSNAYLHSK RNGLLNEALE LTGTPEEEHM GKTTSLIESQ HHHLL HCLE KTTNHEFIDE QMFEQNCMES SMQNYPSTRS PSLSSHPGLT TTCCSRRSKK TTHLPNSNLP ATRLRSMQEL STIHIQ GSE QPSLTTSRSS LNLKADDGLR PNCKTSQITT AIISIPTPPA LTPEGESRPP PASPGPNTNI PSIASNVVKV SALLEGG SS GGWSHPQFEK

UniProtKB: A-type voltage-gated potassium channel KCND3

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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 K2 SUMMIT (4k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 86563
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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